Tony Hillerman's book was the first I was exposed to skinwalkers. Very creepy. But he used the legend in it's real, factual world. Where it is and is not true. Where we get to decide what is true, the white man's science or the legends that the characters grew up with.

I'm mostly with you and Mr Hillerman. If you are using existing mythology, use it and respect it. If not, make clear where you enter the world of personal fiction. I know you don't have to use the references required of academic research in fiction. It would make for some pretty lame storytelling. But if the author chose, an author's note could be included that was believable and research-able. Or made clear where and why the author changed the culture for the sake of story.