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The only reference to the size of a thumb in scripture, in several Upanishads and the Brahma Sutras, is when referring to the atman (brahman) inside the heart of an individual being. I am not aware of any other reference as to Brahman before manifestation being the size of a thumb. What it really refers to is the difference between the spiritual and material dimensions. The Spirit has no physical, no material dimensions, so all souls, all of Brahman can exist within the physical size of a thumb - even less. If I remember correctly the Sanskrit actually says 'no bigger than' the size of a thumb the reference is not meant to imply an exact dimension, it is meant to imply that it has no physical dimension, that the Infinite can exist within the smallest physical dimension.

The Brahma Sutras state in I. 3. 24-25 (Swami Vireswarananda translator):

  1. From the very word ("Lord" by which it is referred to in the text) (the being) measured (by the size of the thumb is Brahman).

[and Shankaracharya's commentary] "The being of the size of a thumb, resides in the centre of the body. (Knowing that) Lord of the past and future, one does not seek to hide oneself any more. This is That" (Katha U. 2. 4. 12). The being referred to is Brahman, because he is spoken of as the Lord or ruler of the past and future. It cannot be the individual soul, though the limitation in size and residence in the centre of the body by themselves might be more applicable in its case. Moreover in reply to the request of Naciketa who wanted to know Brahman, Yama refers to this being of the size of a thumb thus: "That which you wanted to know is this."

  1. But with reference to (the space in) the heart (the highest Brahman is said to be of the size of a thumb); (and because) man alone is entitled (to the study of the Vedas).

[and Shankaracharya's commentary] How could the all-pervading Brahman be of the size of a thumb, as stated by the previous Sutra? Because the space in the heart is of the size of a thumb, therefore Brahman, with reference to Its abiding within that space, is described as being of the size of a thumb. Since Brahman abides within the heart of all living creatures, why is the 'thumb' used as a standard? Because man alone is entitled to the study of the Vedas and to the different Upanishads of Brahman prescribed in them, therefore it is with reference to him that thumb is used as the standard of measurement.

Swami Vivekananda (Complete Works, V2, p 409) says:

Infinitely smaller than the smallest particle, infinitely greater than the greatest existence, the Lord of all lives in the cave of the heart of every being. He who becomes sinless sees Him in all His glory, through the mercy of the same Lord.

Christian theologians in the European Middle Ages had a similar question which perplexed them. The question was - how many angels can dance on the head of a pin? The answer being either 1 or infinite. If angels had physical dimensions, then only one can. If they have no physical dimension, then an infinite number can...

Another good reference to this is Brahma Sutras 1.2.7 (Swami Vireswarananda translator), the verse says that Brahman is referred to as this size for "the sake [or convenience] of contemplation", and commentary "otherwise it is difficult to meditate on the all pervading Brahman".

Also Chandogya Upanishad 3.14.3 "He is myself within the heart, smaller than a grain of rice, smaller than a grain of barley" etc.