In the end, thanks to the easy-going nature of the comic, I can write the whole temporal/multiple parallel timeline problem off as a plot device. I mean, it makes sense if you think about it: If Dr. Light knew that X would at one point return to the past to help Mega Man fix the temporal disruption, it would be logical for him to install components in X to make sure that those events happened.
Another problem that arose from having X in the comic was that it wasn't really mentioned where in the X-series this particular X is from. I believe my original thought was that, since he's still 16-bit and he claims he was just talking to Dr. Cain, it's got to be before X4. The problem with that while we don't don't know what happened to Dr. Cain, we don't necessarily have to assume he's dead by X4, do we?
Further, when we have X and Zero return to the future, we see them revert back into their 32-bit sprites, suggesting that X is only in his 16-bit sprite form here because he's in the present, and that's what bittage the present is in. And considering how Sigma looks when we see X's time period later in the comic, this X is most likely from a time period well after X4 and X5, but before X6.