In Deism, God is supra–cosmic but extra–cosmic, He is on the ‘seventh floor’, all other floors are eliminated, He is not on the other floors, therefore extra cosmic. This reality is supra–cosmic and yet cosmic, therefore He says: “They are in Me”, therefore there is a connection between ‘All’ and the Supreme. The supra–cosmic and all that is in the cosmic they have relationship. But relationship is of such a nature …that can be understood only if you know the relation between ‘essence’ and ‘manifestation’.
The essence always transcends the manifestation. All manifestation depends upon the essence. Essence does not depend upon manifestation; essence may manifest, may not manifest, yet it remains essence, but manifestation cannot manifests without the essence. It is only if the essence exists that manifestation can take place. Manifestation depends upon it; manifestation is in it, in the essence. And yet the essence transcends all that is manifested. There is something in essence that is so great, it is inexhaustible. Even if you multiply millions and billions and billions of manifestations, that essence still remains essence, it is not lost, not exhausted: it is sat. Essence is sat.
This is the sense in which: “They are in Me, but I am not in them”. But also He is in others also. As Sri Krishna will say: bhūtabhṛnna, “I am the bearer of all this, and I am bhūtabhāvanaḥ, I am Myself the whole”: all the statements are together. There is no contradiction because if you understand the idea of essence and its relationship with manifestation then you are bound to say that ‘all are in it’ and yet ‘that is not in them’. At the same time it is true that ‘that is in all’; ‘that is itself all’. But if you look at the essence only, then you have to conclude, (if you look only at the essence, not at the manifestation), then you are bound to conclude, that all manifestation is a manifestation “in the space and time”. Since manifestation depends upon essence, “space and time” themselves depend upon essence: therefore essence is “space–less and time–less”. The entirety of “space and time” depend upon essence, therefore essence must be ‘more’ than “space and time”: it is space–less and time–less.
Now the idea “in”, whatever is conveyed by the word “in” is true only of space and time: the word “in” is only applicable of that which is “space and time”, but that which is “not in” “space and time”, how can you describe of that reality that this is “in” it. Secondly even those which are manifested, even those before manifestation, what is their condition? What is their ontological status: they are also beyond space and time. So, even with regard to them, you cannot say ‘they are in’. You cannot say ‘it is in them’ or ‘they are in it’. Therefore in the stage where manifestation has not taken place, you can make both the statements: “They are in Me”, “I am not in them”, even “They are not in Me”, because the idea ‘They’, ‘They are My manifestations beyond space and time, they cannot be in Me, because the idea of ‘in’ does not apply there.
So, if you grasp exactly the idea of essence which is time–less and space–less and which is also capable of manifesting itself in space and time, then all the statements will fall in their proper place: there is no contradiction. If you want now to describe that Reality, even if ‘you’ want to describe, (not Sri Krishna describing), if ‘you’ the reality which is supra–cosmic but not extra–cosmic, which is supra–cosmic but also cosmic, which is essence but also capable of manifestation, now ‘you’ describe that Reality, you are bound to use these words, namely: “They are all in Me, but I am not in them”, even “They are not in Me”. Then He says: “I am the bearer of all” and yet “I am not in all”, and then “I am Myself all”: mamātmā bhūtabhāvanaḥ.
So, all the statements fall in their proper place: this is the description of the integral Divine. These are the two verses on which, one can write a long commentary.