It’s not like their indigenous identity is respected by Taiwan.

The same reason anyone votes against their own best interests.

Their indigenous identity would be more respected by the PRC is what it comes down to

No, because the Taiwanese Nationalists are ethnically Chinese and want Taiwan to be an ethnically Chinese country.

You can compare it to how more Native American groups supported the British than the Americans in the Revolutionary War: they understood that they would have more autonomy as a minority in a large, multi-ethnic state than a smaller ethnostate.