From the standpoint of the games, the movie is another licensed work - just like the novels, the TV show or the card game. Origin says "you can make a movie in our universe". For Chris Roberts to say it's in "another universe" in the context as director is therefore immaterial to the universe as a whole... since he has no say in what is and is not regarded canon. It'd be like Bill Forstchen deciding to announce that he doesn't consider 'Fleet Action' part of the Wing Commander series. Sure, it's an interesting claim that should be explored... but it doesn't affect the fact that various games consider the events of Fleet Action to be part of their "history".
Consider, also, that the Wing Commander movie relies on the mythos established in the Wing Commander games to exist. It's not something that stands on its own (dramatically or continuity-wise) without background created by the game series. As there haven't been any new WC stories (aside from movie spinoff novels) since the movie was released, we haven't seen it "integrated" into the games histories *yet*.
For now, just leave the movie where it is - an inconsequential little three day event just before the events of the first Wing Commander game.