Well, but remember that the CT events also happened back in the RD dimension, just without reviving Crono, but the rest is like the game, or should I write more correctly, the game itself? I don't see why not.
And just because it happened in another dimension doesn't mean it's not canon, or part of the main sequence canon either. It's just that were are not following it from it's point of view, rather from CC's canon, where indeed is 'another dimension's events'.
Besides, what is Cross, other than RD's 'upgrade', technically speaking?