Interestingly enough, if we can confirm from the RO branch that there are little to no deviations from the IntiCreates timeline until the Elf Wars begins or ends, we validate that both Command Mission and Rockman Zero happen in the same timeline, distancing Zero's ending from the rest of X6.
I don't think that's entirely true, given that XCM itself is a bit disconnected from the rest of the X-series (and being in the next century which caused a bit of MMZ-related confusion among the game's artists). It's very well conceivable to fork during the X8-to-XCM gap.
On that note, one has to raise an eyebrow at RMO's use of Force Metal and continuing to acknowledge its possible side-effects. This is something which showed tremendous promise and yet, presumably due to its dangers, is all but forgotten in Zero/ZX. The older Energen crystals remain dominant despite their poorer performance, even during times of energy crisis when failure to explore other options leads to mass race-killings.