Well, yeah, exactly. J! ships with a specific version of Bootstrap. RT then, as you say, modifies Bootstrap "for their liking". Which is all well and good for them, but ignores the fact that we are all trying to play in the same sandbox. Which is exactly what they did with Mootools.
It wouldn't be impossible for them to modify things in a way which didn't impact everybody else trying to play in the J! space, it just makes life easier for them to ignore compatibility. But while it may save them time and trouble, it simple punts that time and trouble on to others, like us.
-- hugh