I don't see it as him declaring that the movie is a "parallel universe". I think he's just saying that if the diehards want to see it as a parallel, they can.
He does make a point of saying that it all comes down to the end result. No matter how Kirk got to be who he is (serving on the Faragut or not), he is still the same Kirk.
You people have ruined "Star Trek The Next Generation" for me. You are absolutely the most insufferable group of jackasses I have ever had the misfortune of spending an extended period of time with. I hope you all f@*#! die. - Stewie after spending the day with the TNG cast.