OK, this is a huge and long standing pet peeve of mine, so let me say it again.
THERE WAS NO NATIVE AMERICAN CULTURE.
Rather, there were a host of Native cultures, vastly different, ranging from highly 'civilized' (in terms of urban living, agriculture, political associations and languages) to extremely primitive, almost Stone Age.
To lump all of them together is to do a disservice to all. So, where some cultures revered 'two spirit' that practice was not universal by any means. We can find the practice in some (but not all) of the Southern/Southwest cultures, but not at all in the Northeast or West. Some of the historical records even indicated that in some tribes, far from being 'revered' they were held in very low esteem, and often faced outright prohibition.