True, actually hacking the rom--the game's core components--seemed to be SE's biggest beef, although granted that wasn't the only issue. At any rate, I also doubt any big-wigs will be out to chop down a fan-brewed RPGMaker project, since there are scores of them already, much like glorified fanfics.
So, I just beat Chrono Alter yesterday and found this new game underway. I'll be keepin' my eye on this to see how it goes.