I understand the completionist mind-set all too well, and have only recently taken to accepting some things don't fit, or even if they do fit, aren't meant as canon.
I look at it like this: if a series of comics, like say #1-50 of a given series, didn't fit within another series' canon (even if 49 issues did but one didn't), ideally, from a canon point of view, it kind of negates the entire series from that established canon. While the X2 prequels are different one-shots, they all fall under the same "series", as in a series of one-shot prequels related to X2.