I'm looking for manga about indigenous people of any nation (although I'm especially interested in Ainu), preferrably portrayed in a respectful and well-researched way. Does it exist?

I haven't read it... but just from the cover alone, I'd love to get my hands on a copy. Yamataika

Now, you already posted in this thread; so, I know you know about it. But, I'm adding it for others to check against.
http://www.mangaupdates.com/showtopic.php?tid=19440

Yuki's Sun might work.

________________
"Officially, this machine doesn't exist, you didn't get it from me,
and I don't know you. Make sure it doesn't leave the building."

Otoyomegatari, though it seems you're already reading that. ^^