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.
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...