The inherent bhakti-vādis claim that Vedānta-sūtra 4.4.1 shows the inherence of the siddha deha inside the ātmā. Śrī Babaji has refuted this incorrect idea in his book, Jīva tattva. I reproduce his refutation below.
On the basis of Vedānta-sūtra (4.4.1) and its commentary by Śrī Baladeva Vidyābhūṣaṇa, some argue that a spiritual body has always existed within the ātmā and upon liberation it is revealed. Below we will discuss the argument that has been made in favor of this position after first presenting a complete translation of Śrī Baladeva Vidyābhūṣaṇa’s commentary on the sūtra, which consists of an introduction, a counterargument (pūrvapakṣa), and a commentary resolving the doubt under discussion.
In this quarter of the Forth Chapter of Vedānta-sūtra, the svarūpa of liberated persons and their experience of enjoyment is being described. There is a following statement of Prajāpati:
evam evaiṣa samprasādo’smāt śarīrāt samutthāya paraṁ jyotir
upasampadya svena rūpeṇābhiniṣpadyate sa uttamaḥ puruṣaḥ
“In this way, receiving His mercy, rising from his present body, having approached the supreme light, he is accomplished with his own form. He is the best person.” (Chāndogya Upaniṣad 8.12.3)
Here arises a doubt: Is this “accomplishment with one’s own form” a relation with a perfected form, just as one can have the form of a deva, or is it a manifestation of one’s own natural form? [When one attains one’s “own form,” is that perfected form external to the self, like the form of a deva or human being, or is it the natural form of one’s ātmā?]
This form arises as a result of practice because the word abhiniṣpadyate [in the mantra cited above] has been used [“abhiniṣpadyate” means “to attain or to accomplish”]. Otherwise this word would become meaningless. Furthermore, the śāstra dealing with liberation would not teach that this is the goal to be achieved if it is accepted that this form was naturally related to the ātmā. This is so because this svarūpa would have been present prior to the attainment of perfection and would thus not be seen as a goal to be achieved. Therefore, the conclusion is that the meaning of the word abhiniṣpadyate is “to have a relationship with a form to be achieved by practice.” [Here ends the introduction to the sūtra and now the sūtra and the explanation given below will resolve the doubt and refute the argument stated above.]
Sampadya—of he who has attained; āvirbhāvaḥ—manifestation; svena—by one’s own; śabdāt—understood by the word.
Of the one who has approached [the supreme light], there is a manifestation [of the svarūpa] because of the word svena.
The special state characterized by the appearance of one’s svarūpa, which is free from the bondage of karma and endowed with eight characteristics, is called “manifestation of the svarūpa (svarūpa-āvirbhāva)” of the jīva who has attained the supreme light through bhakti assisted by knowledge and renunciation. Why do you say so? This is because the sūtra uses the word “svena.” The meaning is that the word “svena” here is an adjective of the word “svarūpa.” [Thus, it means “with his own original nature.”]
If it is accepted that the jīva gets a form from outside, then the word “svena” would be futile. Moreover, even if the word “svena” were not used, the word “svarūpa” itself would convey that the jīva gets his own form. [Thus it is proven that the jīva gets his own form and not something external that is affixed to the jīva.] The word “abhiniṣpadyate” is also not superfluous, for this word is also used in the sense of “is manifested.” An example of such a meaning is seen in the following sentence: idam ekaṁ su-niṣpannam, “This one has manifested properly.”
It also cannot be argued that because this form was pre-existent, it cannot be a goal of human endeavor, because it did not manifest before [this form only manifested after success in sādhana, therefore it can be goal of human endeavor]. It also cannot be said that then the practice taken up by the person would be fruitless, because it is useful in manifesting it.
Here some explain that the word “niṣpatti [niṣpadyate]” means “the attainment of a state of dissociation from all material sufferings caused by the superimposition of prakṛti by the ātmā, which is self-luminous, pure consciousness, and is supremely effulgent by nature.” [This is the view of the Advaitavādīs, who do not believe in the attainment of a spiritual body and consider liberation to simply mean becoming free from material conditioning.] This is not true, because the Śruti declares that in that state of liberation one [also] attains supreme bliss: rasaṁ hy evāyaṁ labdhvānandī-bhavati,“The living being becomes blissful only by attaining Rasa [Bhagavān].” [End of commentary]
The point of contention in regard to this sūtra and the commentary on it is the meaning of the manifestation of the perfected jīva’s “own form” (svena rūpena). The sūtra uses the word āvirbhāva, which means that this form becomes manifest. In the Bhāgavata verses cited earlier, the words used for the siddha-deha attained by a jīva were prāpta, āpa, lebhe, dadau, rāti, and so forth, all of which mean that the jīva’s siddha-deha was either attained or given. There was no mention in the Bhāgavata of terms such as āvirbhāva or prakata, which mean “to manifest,” as used in the present sūtra. On the basis of this description that the jīva’s own form is said to become manifest, some assume that the form alluded to in this sūtra is the perfected form (siddha-deha) a jīva attains by following the path of bhakti and then argue that this perfected form must be pre-existent within the ātmā because it is implied to be so by the statements in the commentary which say that at the time of liberation, this form becomes manifest. Proponents of this view consider that their interpretation is further supported by the word svena in the sūtra itself, which means “his own.” Thus from this sūtra, they draw the conclusion that when a perfected jīva becomes liberated, a spiritual form becomes manifest from within the jīva and therefore the siddha-deha is inherent in the jīva itself.
First, we should note that the sūtra as well as the Chāndogya mantra cited in the introduction to the sūtra are silent about the location of the spiritual form before it becomes manifest. The location can either be within the ātmā, as is contended by the opponents, or it is in the spiritual word.
If it were accepted that the svarūpa mentioned in this verse refers only to a siddha-deha that lies dormant within the jīva and then becomes manifest at the time of liberation, then a contradiction would arise with sūtra 4.4.12. The sūtra states, “Because [a liberated jīva is satya-saṅkalpa, or one whose wish comes true], in the opinion of Bādarāyaṇa, he can be of both types [with or without a body] just like the twelve days’ sacrifice [can be both an Ahīna or a Satra].” The intention of this sūtra is that there are two types of liberated jīvas. Those who follow the path of jñāna attain impersonal liberation, brahma-sāyujya. They do not receive or manifest a siddha-deha because they perform their sādhana with the resolve (saṅkalpa) to identify with Brahman. In their case, manifestation of the svarūpa as described in sūtra 4.4.1 simply means manifestation of their pure spiritual nature as a jīva possessing the inherent characteristics discussed in Chapter 1. If followers of the path of jñāna were to be given a spiritual body (siddha-deha), or such a spiritual body were to become manifest from within, then they would identify with this spiritual body instead of Brahman. Thus, they would not achieve the goal for which they performed their sādhana and a contradiction would arise with the meaning of sūtra 4.4.12.
The second type of liberated jīvas are those who follow the path of bhakti. They attain a spiritual body (siddha-deha), which they then identify with. They perform sādhana with the resolve to serve Bhagavān, and in order to render service to Him, they need a spiritual body. Thus, they are granted one, unlike the followers of the path of jñāna, who are not granted such a body. So, in the case of followers of the path of bhakti, manifestation of the svarūpa as described in sūtra 4.4.1 means their attainment of a siddha-deha.
Mukti is defined by Śukadeva Gosvāmī as giving up an external form and becoming situated in one’s own form (svarūpa), muktir hitvānyathā rūpaṁ sva-rūpeṇa vyavasthitiḥ (SB 2.10.6). While commenting on this verse, Śrī Viśvanātha Cakravartī mentions that this verse refers to two types of perfection, one that is attained by followers of jñāna-mārga and one that is attained by practitioners of bhakti.
Sūtra 4.4.1 thus does not discriminate between these two types of practitioners and rather speaks so as to describe them both. If a siddha-deha were dormant within every jīva, then it would become manifest for both types of practitioners. However, if a supposedly dormant siddha-deha were to become manifest for a person who wants to attain brahma-sāyujya, or impersonal liberation, it would go against his resolve. Moreover, such a circumstance is not heard of or accepted by anybody. Furthermore, it would make any attainment of brahma-sāyujya an impossibility and thus contradict all the statements in śāstra which speak of brahma-sāyujya as a real and permanent attainment. Therefore, it must be accepted that there is no siddha-deha dormant within the jīva, and rather that a spiritual form is given at the time of liberation to devotees, that is, those who have performed the sādhana to attain that. This is the intention of sūtra 4.4.1. The word used is āvirbhāva, or “manifestation,” and the intention is not that the spiritual form manifests from within but that it becomes manifest to a perfected bhakta when it is bestowed upon him from without.
Here a doubt can be raised: If a person who attained brahma-sāyujya does not obtain a form, how can sūtra 4.4.1 be applicable to such a person? The reply is that sūtra 4.4.1 is simply saying that in this case, the jīva manifests his own nature, or svarūpa. The word svarūpa, which has two meanings, “nature” and “form,” is meant to be understood as “nature” for the jñānīs and as “form” for the bhaktas. This is evidenced in Śrī Viśvanātha Cakravartī’s commentary on the definition of mukti cited earlier wherein he explains that the svarūpa which manifests to jñānīs is simply the pure nature of the jīva whereas the svarūpa that manifests to bhaktas is the form of an associate of Bhagavān. Thus in the case of brahma-sāyujya, a liberated jīva reaches the state of existing solely in his spiritual nature (svarūpa) of pure consciousness, and in case of personal liberation, the jīva is given a spiritual form (siddha-deha). This conclusion is confirmed by sūtra 4.4.12.
Furthermore, if we were to accept sūtra 4.4.1 to mean that a siddha-deha is dormant within every jīva, then that would contradict all the statements of Bhāgavata Purāna cited earlier, which state that a person who attains prema is given, that is, receives, or attains, a spiritual body. In this regard, we should remember that Bhāgavata Purāna is the natural commentary on the Vedānta-sūtra by the author himself. This is said in Garuḍa Purāṇa, pūrṇaḥ so’yam atiśayaḥ, artho’yam brahma-sūtrāṇām, “This [Bhāgavata] is the most complete of the Purāṇas. It embodies the essential meaning of the Vedānta-sūtra.” While commenting on this, Śrī Jīva Gosvāmi writes:
In the above statement, the phrase “[Śrīmad Bhāgavata] embodies the essential meaning of the Vedānta-sūtra” (brahma-sūtrāṇam arthaḥ) means that it is tantamount to being a natural commentary (akṛtrima-bhāṣya) on the Vedānta-sūtra. The Bhāgavata first self-manifested in a subtle form to the awareness of Śrī Vyāsadeva, who then summarized it in the form of the Vedānta-sūtra and later expanded it into Śrīmad Bhāgavata as we know it. Therefore, since Śrīmad Bhāgavata self-evidently embodies the natural commentary on the Vedānta-sūtra, all other recent commentaries, sprung from the fertile imagination of their authors, should be honored as authoritative only when they are in resonance with the version of Śrīmad Bhāgavata. (Tattva Sandarbha, Anuccheda 21)
Here Jīva Gosvāmī writes very clearly that Vedānta-sūtra must be understood in the light of Śrīmad Bhāgavata. Any understanding that contradicts Śrīmad Bhāgavata is certainly a “fertile imagination.” Therefore, on the authority of the Bhāgavata, we must accept that the āvirbhāva of the spiritual nature or form mentioned in sūtra 4.4.1 is not from within but rather is a manifestation from the spiritual world. Since the sūtra does not say clearly that the form manifests from within the jīva and the Bhāgavata is clear that it is not from within but given by Bhagavān, we have no choice but to accept that the manifestation, or āvirbhāva, is from the abode of Bhagavān and not from within the jīva. There is no other possibility. Indeed, this is the meaning of the verb abhiniṣpadyate in the Chāndogya mantra 8.12.3.
Another doubt may be raised: In the commentary by Śrī Baladeva Vidyābhūṣaṇa, it clearly says that the svarūpa which manifests is not adventitious, or external. This implies that this form must be within the jīva.
Reply: Here, it should be understood that the meaning of the word āgantuka (lit., “adventitious or external”) is that the svarūpa that the jīva attains at the stage of perfection is not external to the jīva as the material body is. Whether the meaning of the word svarūpa is taken as “nature” or “form,” both are one with the jīva and not something foreign or external to him. Why? Both the jīva as well as his spiritual nature or spiritual form are conscious by nature and not material. This is the significance of the word svena, which is a modifier of the term svarūpa. The meaning therefore is that the spiritual body received by perfected devotees is one in nature with the jīva in the sense that they are both conscious by nature and thus not āgantuka, or external. Here in the material world, the material body and the ātmā are two distinct things and therefore there is duality. However, in the spiritual world, the ātmā and its body are both conscious and act as one unit. Therefore, there is no duality between them and thus no duality in the spiritual world. Because the material body is inert and the ātmā is conscious, they can never be one. Thus, the material body is called “the second,” or dvitīya (SB 11.2.37). The meaning is that the material body is āgantuka—adventitious or external to the jīva’s svarūpa. It is to deny this “second-ness” of the spiritual form realized in perfection that the sūtra 4.4.1 states that this form is one’s own svarūpa. Further, the intent in saying here that the spiritual form “manifests” is to convey that it is not created. Thus, the sūtra does not say or imply that a siddha-deha was pre-existent in the ātmā.
 The eight characteristics are freedom from sin, old age, death, grief, hunger, and thirst, and having one’s desires fulfilled and all one’s wishes come true.
 jñāna-vairāgya-niṣevitayā bhaktyā paraṁ jyotir upasampannasya jīvasyeha karma-bandha-vinirmukta-guṇāṣṭaka-viśiṣṭa-svarūpodaya-lakṣaṇo’vasthāna-viśeṣaḥ svarūpāvirbhāvaḥ kathyate | kutaḥ ? svena-śabdāt | sveneti svarūpa-viśeṣaṇād ity arthaḥ | āgantuka-rūpa-parigrahe’narthakaṁ tat syāt | asaty api tasmin tasya svakīya-rūpatva-siddheḥ | na cābhiniṣpatti-vacanaṁ vyartham | idam ekaṁ suniṣpannam ity ādiṣv āvirbhāve’pi tac-chabda-vīkṣaṇāt | na ca tasya pūrvaṁ sataḥ pumarthatvaṁ na pratītaṁ tādṛg-avasthāyāḥ pūrvam anudayāt | na cātropāya-vaiyarthyaṁ tad-udayārthatvena sārthakyāt | yat tu svaprakāśa-cin-mātrasyātmanaḥ paraṁ jyotir upasampannasya nivṛtta-nikhila-prakṛty-adhyāsa-duḥkhatayāvasthitis tan-niṣpattir ity āhus tan na—rasaṁ hy evāyaṁ labdhvānandī bhavatīti muktāv ānandātiśaya-śravaṇāt ||
 When there is more than one host for a twelve-day yajña, it is called Satra. When there is only one host, it is called Ahīna.
 dvādśāhavad ubhaya-vidhaṁ bādarāyaṇo’taḥ
 anyathā-rūpaṁ māyikaṁ sthūla-sūkṣma-rūpa-dvayaṁ hitvā svarūpeṇa śuddha-jīva-svarūpeṇa, keṣāñcid bhagavat-pārṣada-rūpeṇa ca, vyavasthitir muktir iti.
 brahma-sūtrāṇām arthas teṣām akṛtrima-bhāṣya-bhūta ity arthaḥ | pūrvaṁ sūkṣmatvena manasy āvirbhūtaṁ, tad eva saṅkṣipya sūtratvena punaḥ prakaṭitaṁ, paścād vistīrṇatvena sākṣāc-chrī-bhāgavatam iti | tasmāt tad-bhāṣya-bhūte svataḥ-siddhe tasmin saty arvacīnam anyad anyeṣāṁ sva-sva-kapola-kalpitaṁ tad-anugatam evādaraṇīyam iti gamyate.
 Although the jīva is part of the taṭasthā-śakti and the siddha-deha is part of the antaraṅgā-śakti, and they are thus distinct from each other in exact constitution, in the context of the present discussion of Chāndogya Upaniṣad their oneness in both being of conscious nature is being emphasized and distinguished from the material nature of the physical body.