I thought it was obvious from The Movie (as you put it) that a large part of the story would be how "he came along" mattered and how that changed things. The biggest thing that changed was Brian and Justin becoming a couple (if a nonconventional one) and how that changed them individually. This being said I didn't see it as necessarily meaning just about Justin or just about Brian changing or just about Brian/Justin.
One issue I sometimes have with "what if" stories is that changing one thing can have unintended consequences. Brian changed because of Justin and his relationship with Justin. This changed how Brian interacted with Michael, Ted, Lindsay, Gus, and the rest. Likewise Justin's story is not just about Brian and their relationship. However, had 101-103 been a movie due to time constraints it would have been more B/J focused than the show as a whole as the writers would have had to stick to the basics. Also had it been a movie I think the other characters would have gotten less screentime. The writers knew that they were introducing characters who would be focused on more later.