Seemingly Positive Stereotypes
I think I've figured out one of the real problems with those stereotypes. It's a matter of the perspectives they suggest. When you think of a 'noble savage' or an 'innocent retard', you typically don't think of that hypothetical person from xyr own perspective. You think of these people from the perspective of an observer. And how would you go about understanding their perspectives? You can't ask them - the 'innocent retard' would probably not understand the question, while the 'noble savage' would reply in some riddle you can't understand. At least, that's the perception, and comments from people viewed in the lenses of those two stereotypes will be interpreted in those ways.
Native people and disabled people are not like nondisabled whites. We all have things in common, sure, but there are also differences, and often the stereotypes catch an element of those differences. But they hide the most important perspective on that group - their own. If your stereotype is of someone you can't imagine being, yet can predict the actions of, then it's probably not a stereotype that the people described will be happy with.