"the base of setting and character design"
Isn't that basically the core for the entire IoMioE and the characters aka how she looks like, talks like, acts like, behaves like (traits etc)? How is that canonically questionable?
What Helepolis said. Canons are fundamentally dictated by the ones who "own" the property in question, in this case, ZUN. Thus, the usual stance would be that only what he directly writes is canon. However, if ZUN were to officially acknowledge that Inaba Inaba is indeed part of his official Touhou canon, then that would also be the same thing.
Don't get me wrong, I'm highly open to the idea that Inaba Inaba is indeed canon. However, as long as there's an iota of a possibility that it's not, I'll be hesitant to accept it as such. But that's just me, of course.