The spoken and written language are not the same thing. Even if you say "Thomas's," sources disagree on whether you write "Thomas's" or "Thomas'", because the latter is more consistent with the rules for other ends-in-s words and, therefore, easier to remember.

(My personal prediction: give it 100 to 200 years and we're going to drop the trailing 's' in all these cases. "Cat'" will just be pronounced "cats" and understood to mean "an adjective indicating the noun is owned by the cat").

Thomas’ is pronounced the same as Thomas’s.

As the OP said, "Thomas'" is pronounced "Thomases".

"Thomas's" means "belongs to Thomas". Pronounced the same, but spelled differently, because it is a different word.