I wasn't so much thinking of their exclusion as I was thinking of the direct linking of Zero's sealing to the Nightmare Incident.
In Rockman Online, Zero actually acknowledged himself as a host, yet we hear no sign of his seal. That would certainly fit such notions. Furthermore, we always had some issues keeping XCM within "XX" years.
As such, the question I must raise... does X7+ Zero acknowledge himself as a host of the virus?
A highly questionable part of this, though, is how a split based in X6 would work. The in-game continuity split of whether or not X locates Zero doesn't match the issues we're having between MMZ, XCM, and RMO. Zero seals himself for an expected (may or may not be actual length) 102 years after being located by X, which can only fit with MMZ. And he leaves for an unknown reason if X does not locate him.
Both roads could conceivably lead to MMZ but neither work without it; Zero needs to drop off the radar at some point in the storyline one way or the other. MMZ's backstory is the only account of that happening. It's definitely RMO's responsibility, then, to offer up some explanation. Which I'm sure they intend to do if they're offering Cinnamon's visions of Neo Arcadia as a plot point prior to game release.
Bear in mind, with X6's Zero ending, the reason for displacing it from the rest of the game is two-fold. One is, obviously, to make room for sequels. But the other, which must not be overlooked, is that there is no lead-in concerning it among the game's other events. The ending is extremely ambiguous and is not cross-referenced with any other X6 event, with the inverse also being true in that the ending itself makes no reference to Gate, Sigma, and the like. Further, there is no event specific to X6 which identifies Zero as the virus host; if anything Zero's most significant information at that point in time would have come from X5, thus remaining constant across all possible forks of X6. This is why I maintain, that the ZC timeline referencing the Nightmare as cause of this knowledge suggests that the incident was re-examined at a later point (X salvaging Gate's body certainly leaves a window open, research-wise, if nothing else).
That would make me question why Zero believed it even would work.
I would chalk it up to "limitless evolutionary potential", the same technology used for his special weapons. That would make other Repliroids incapable of it, but Zero has seen it at work before, making him sure of its feasibility.
Between VWS and X's other armor parts, yes, Zero should be well aware of X's ability to assimilate the abilities of others. This also conveniently dodges X and Zero comparing the Z-Buster and spiral-buster since in that fork they'd have never seen the latter. BUT, I have to raise an eyebrow at the Z-Buster enabling charged special weapons. That's not tech that Zero should have, which seemingly further implicates some crossover with Light during development. There's also the fact that X's non-bustered arm responds to the upgrade, not typical of VWS weapons.
One thing that interests me here is that they acknowledge Command Mission alongside Inticreates' scenario of host Zero and Sigma Virus' deletion by X to end the Irregular Wars, without inevitably leading into Rockman Zero. Apparently there's no real conflict between Command Mission and Inticreates' story with these basic details.
If we accept that at face value, then we're looking at the time-split being grounded at the pre-Elf Wars seal. I don't think it can be much later than that unless we see a baddie copying Omega.
...it occurs to me, Omega's existence defies reality and ruptures the border with cyberspace where all the world is data. He could very well be key to such reality warping as a branched universe making contact between the branches. *PURE* speculation on my part, obviously, but it's fun to think about.
Traditionally, we've only ever considered timeline splitting because of gameplay input leading to alternate endings. With X7 and beyond giving us little of that, it seems natural to focus on X6. Does it not?
See above. X6's split does not mesh with the story details we have on the table. In a MMZ-less continuity we have no account of Zero dropping off the radar, which is a necessity in both forks of X6.
There's also the fact that X7 foreshadows MMZ. Unless we're to assume that Zero and Snipe Anteater have some lesser version of Cinnamon's visions, anyway.
The beauty of branching timelines compared to a completely different continuinity is that we can reason Axl and the Copy Chip would exist before the story splits ways, justifying ZX Advent even if a story like X7 never happened.
Touche, such thoughts have occurred to me when brainstorming possible futures off of X5's alternate ending.
That said, while the tech certainly would progress and Axl most likely still existed in some form, Zero's presence was pretty key to putting Axl on the map, in terms of the history books. While Albert pulling the Copy Chip tech is logical in any event, pulling Axl as the design/combat inspiration is a bit more iffy.