As Jeff Zeitlin mentions in a comment on Ghotir's answer, GURPS does not differ from the OTU beyond the "alternate timeline" issue.
In fact, since Loren Wiseman ran that line, GURPS material is generally quite good. And when its books treat a general OTU topic, they do it so well that the material is often a very nearly GOLDEN canon source. For example, the Sword Worlds book is as canonical as it gets. It's nearly perfect (although it's a little dry for my tastes). If I had a canon question about the Swordies, I'd go to GURPS. Ditto for Starports.
But... sometimes the assumptions go too far for my comfort -- for example, Behind the Claw is spurious (fact, not my opinion), and Far Trader relies too heavily on Terran economics, losing sight of the game (my opinion).
Largely though you can ignore that. If you have GURPS, and you use GURPS with an MGT2 game, you're going to be fine.