hm.. well i cant argue too well on x and megaman but it seems that from the interview that keiji (creator of megaman) was pretty clear that there is a distinct difference and they will be avoiding the x and megaman relationship

btw where is the source of that? are you sure its not just a fanfic?

here is the manual and script for mmx1.. no indication of the paragraph you mentioned and additionally the manual seems to use X in all places and avoids most things in connection to the old mm series
correlating with the interview sentiment of avoiding linking them together directly:
http://megaman.retrofaction.com/mmx/...mmx1manual.php
http://megaman.retrofaction.com/mmx/...mmx1script.php

in mmx1.. final sigma has a mode where you see him holding a large gun popping out of the upper right.. when he says "the end" he shoots a laser ray that hits against the floor and causes kind of an explosion on the ground.. if x is on the floor he dies instantly