So true xueens and xings! Mayocide when?!?!?!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100129/

This is the only reference I could find.

Hermaphrodites and cross dressers are mentioned in some texts.

There's also references to krishna's son dressing as a woman to conduct espionage in the court of an asura king.

The most common references to gender neutrality seems to be descriptions of God[neither male, nor female, nor ali(transgender) ] etc etc in the usual negation structures used to describe nirguna brahman(God without attributes)

From what limited tamil sources are available, we could say that transgenders/hermaphrodites were just thought of as a third gender. There's no evidence that it was widespread, just that it was acknowledged to exist.