Wario hasn't appeared in any "major" Mario game since SML2, not even the RPGs, so it seems to me that him and Mario don't see each other that often, except for the spin-off games, and rare instances like SM64 DS, if you consider it canon. Now with his new company and everything, he probably spends a lot of time in the Diamond City area making his games (or rather, forcing his employees to make them). Mario does seem like the kind of person who would forgive Wario for stealing his castle and everything, however, seeing as Wario hasn't done anything nearly as villainous since then, so when Wario is around, he and Mario should get along fairly well.
I'm not very fond of the whole "fanon" concept, if the truth must be told, especially since I'm a "conformist" fan-fiction writer (if that's the right term). I tend to avoid what's already in the games, such as continuity discrepancies. The games are my only source of information, and I don't make up any information Nintendo hasn't revealed to us (my project on this forum is the exception to that last one).