I don't think any of that makes much sense... I'm not criticizing your thinking, it's not your fault that the writers didn't think any of it through or, at least, didn't bother to explain it. This stuff with Mastermind reads to me as just some excuse to create some drama/conflict for an otherwise thin plot.
Personally, I'm tried of this whole dual-personality stuff. Writers have relied on it way too much to create personal drama for Warren. And the whole back and forth on whether he's mended his mind or it's split again has got old. Let him be able to morph his wings (morph his skin with it if people really want him to be blue) and have a moderate healing factor and give him his personality back. Warren on his own is so cool. I miss him. This character we saw in the first 2 issues of X-Corp is pretty bland.
But then again the story is pretty meh. How many issues will it take to form the board of the corporation on a book called X-Corp? Seriously. This is silly. Imagine if the new X-Men book took three issues dealing with the election of X-Men team...