Regarding canon, I think it's usually understood what canon someone is talking about from the context, but I'll admit it does appear to get to be confusing for newcomers to the fandom. If I recall, at one point Mega Man Network had an article explaining it, though I think it got dropped over subsequent site moves/reboots, along with their Sourcebook info section.
As for Japanese Rockman canon vs American/European/etc Mega Man canon... While some things are apparently changed intentionally for western audiences, a lot of Mega Man game and media produced info suffers from inconsistency, misconception and mistranslation. Where we can't always tell which is what, it is easier (for those familiar with the Japanese versions at least) to go by the original standard and note the exceptions. But outnumbering these are the many games, books, cds and merchandise that were never brought over at all, and thus regional counterparts don't exist. If we say that American game canon is a separate entity from Japanese game canon, then we essentially say there is nothing in the Japanese canon that applies to the American without being expressly mentioned in the American. Which means huge gaps and a large number of unknown variables that would otherwise have been understood.
I don't think this is news to anyone in this thread, hell, much of this thread itself is proof positive of what I'm referrring to. And that's not to say Japanese sources never contradict, never retcon or never offer silly explanations that don't necessarily make the most sense. It isn't about what's "best," you can prefer whatever version you like, be it manga, comic book, anime, cartoon, A-game or J-game. There's always the option to compose your own fanon or exercise your imagination regardless of any of these.
What the default phrase of "canon" usually refers to around here is that these are stories and backgrounds put out by the people who first and foremost created these games, this is the tale they told before it was wrung through the filtering process for another region, or reworked into a comic book or TV show, and this is the foundation that future game and related entries are likely to build from and abide by (for whatever that really accounts for). I usually try to specify "game canon" even though that itself is something of a misnomer in that it actually extends further than what is simply found in the games. But because it's mostly what I talk about, what I think most of the plot discussions in this entire board section are about, it's simple enough to just say canon for shorthand. When we're talking about a different canon, manga for instance, it usually requires further specification anyhow, as in "Iwamoto's Rockman X manga" which is mutually exclusive with "Ikehara's Irregular Hunter Rockman X manga," or "Battle Story Rockman EXE manga" vs regular "Rockman EXE manga" vs. its American counterpart "Mega Man NT Warrior manga" etc. etc. etc. To refer to them all commonly as "canon" would, in my estimation, be more confusing than the current state where one recognized version is regularly referred to as canon and the others as specified as separate universes, which though not necessarily mentioned as such are understood to be canon only to themselves.
Anyway, the cool thing about Gigamix is that practically no one in the Capcom licensed manga realm, not even Ikehara, has done a serious R3 manga before. And for that matter, most "sourcebooks" from that or any current era skip over the greater part of the details about the unknown worlds, Blues/Breakman, the crystals and Gamma... For such an old game, it's new territory. It will be food for thought, if nothing else.