>

The ones you call "gender scholars" are cultural anthropologists, and whether you personally agree or not does not change that these same scholars might adopt another word due to all the misinformation and controversy surrounding the word.
I mean, there are many articles about this.

That would assume modern gender theory is built on or borrows from a culture (in this case - a wide variety of indigenous cultures) that "gender scholars" (which are barely even a thing anyways) have little understanding of or experience with.

You are treating gender as a hard science, which it is not. Gender is a social construct, and relies on the culture it exists in. Experience in one culture does not always translate to another.
You are also assuming scholarly work is always objective and impartial. If it was, Academia would not push this. It exists because anthropology is flooded with old thinking that effects the ability of anthropologists to study culture.
This is an area of history where the papers published is really low, and some cultures havent had papers written about them in a very long time, sometimes decades. These are cultures historians were calling "stone age savages" as late as the 1950s. 
I think you realize the problem this is trying to solve.
Sadly this is the situation with many native/indigenous communities across the Americas. >

Indigenous communities have been fighting for centuries but still get massive backlash and hostility.
You cant even talk about indigenous political stances because decolonization politics attacks the foundations of pretty much the entire political world.
Say Identity Politics in the Americas has roots in racial essentialism and erases indigenous culture to just "genetics", and that gender theory appropriates indigenous concepts like two spirited people without actually understanding the concept and you get in trouble with people who talk over feelings of Indigenous people.
Its hard to find political support when there is so much institutional hostility and these institutions literally do not think of the world the same way. An interview with an indigenous author had the interviewer ask if she was not "happy civilization lifted everyone out of poverty" instead of being pro-environment.
For many people, indigenous communities are still "in the way". >

Could you explain how "non-indigenous" gender theory appropriates indigenous gender theory? I've never met a 2S person who thought this way about it at all. >

I'm familiar with this history, but I still don't see how it equates to non-indigenous gender theory appropriating indigenous gender theory. That would assume modern gender theory is built on or borrows from a culture (in this case - a wide variety of indigenous cultures) that "gender scholars" (which are barely even a thing anyways) have little understanding of or experience with. This isn't the case though, and modern non-indigenous "gender theory" is primarily a collection of ideas from trans people about their place in their societies and cultures. Some number of non-indigenous people trying to understand two-spirit identities without the specific cultural background is just not appropriation, and it isn't even part of a wider gender theory.