I've just started re-reading the system, so I can't really offer many thoughts on the Transcholar. I do like the Transcendence capstone working in all the required principles, but on the other hand it seems like a lot of required principles - at least at first glance. You only get five principles that are freely chosen if you obtain all of the Applied Focus ones, and while there aren't that many principles to begin with (and so five is still rather a lot) that's still an awful lot of choices to be locked in.
I also think you meant to say in Transcendence that if you used IMCH388 you can spend uses of Minor Virtuality to become fully corporeal, since you're already incorporeal at that point. Unless I'm really missing something, which is entirely possible.
However, mostly posting to give an idea for a GEOC/IMCH combination prestige class with a capstone which allows it to trick Geoccultic Poles into thinking they have more mass than they actually do (for the purpose of critical mass, expending mass for upkeep and such) - probably called World of Pure Imachination. Partially putting this here so that I remember it if I take up making such a prestige class once I've finished re-reading, and partially to put the idea out there if anyone else would like to use it (I don't mind).