I view Judgement as in the same vein as Capcom Vs SNK, King Of Fighters, Capcom vs Tatsunoko, NeoGeo Battle Colliseum, and the like.
I mean, really, a guy can spam fireballs out of his hands and people are pissing themselves about someone a guy wearing spandex with a high-tensile liquid grappling compound hidden under his sleeve? (MvC) You mean Nakoruru could be one of Athena's biggest fans? (NGBC) Epic showdown between Chun-Li and Haohmaru! (CVS)
Hell, even KOF series has continuity issues that prove the game series isn't canon to anything, just a mash-up of other games. (Although back when Mai and Andy were both staple characters, there was some continuity there, but that was about it). ... Hell, Clark and Ralph don't even recognize each other anymore! (Has to do with Playmore sucking ass, more than anything.)
So no, I don't think it's canon. I think IGA is just trying to make Judgement sound like it's not simply another mash-up. But it is. All mash-ups have shitty plot excuses to explain why everyone's together. MvC3 had the intro video to do that. Hell, though. At least SNK never really gave a shit. They're like, "Yeah, we'll mix a bunch of characters together from various franchises and have them fight to stop a powerful enemy. How did they all come together? Fuck it, who cares?"