I can think of a reason why it wouldn't have worked in canon, and it actually has nothing to do with Brian and Justin as characters, for me.
It has to do with Leda.
Leda is a pivotal character, but her role in QAF was not to trigger something for Brian and Justin. She was there for two reasons: to tell us something about MELANIE, and to trigger something for Melanie and Lindsay, and their relationship.
The fictional purpose of that exchange with Brian about "ever been fucked by a dyke with a dildo?" wasn't to speculate on whether Brian and Leda would have sex, but to show us that Brian and Leda were "birds of a feather," in order to tell us something about Melanie and her past. Mel's reaction.... "would the two of you for once shut your dirty mouths?" demonstrates that very clearly. We are learning about Melanie there, not about Brian.
The dancing and playing at the party after everyone did E was also to tell us about the confict between Lindsay and her parents, and demonstrate the difference between the happy, playful world of, well, dancing and drugs and sex, where everyone is engaged in polymorphous perversity and has no hangups and doesn't take everything OMG SO SERIOUSLY.... which is, IMO, the message of this story arc for Lindsay, and the meaning of her conversation in the bedroom with Brian... and her parents' uptight, cold, WASP world.
To take that and turn it into being about Brian and Justin, which it clearly isn't, drags the story away from Melanie and Lindsay, whose story it is.
Now... that's canon. Lots of fic takes things from canon and drags it off in a "what if" direction, according to the author's (or bunny-requester's!) desires. This thread started by jameserin, which is about canon, and the discussion of your bunny, which is about a fic, aren't really about the same thing, nor are my feelings about canon and my opinion on a fic bunny the same.
Here's an example of how I see it. I have a fic kink for Brian carrying Justin, and my view on what's "in-character," while it doesn't bend far, might bend a teeeny bit further in service of that kink than in some other situations, LOL. I still have to believe it... an author can't just "make it so" and have it satisfy me.
Brian and Leda and Justin having sex *in canon* is not in character for them as characters and, more importantly, it deviates very strongly from the role Leda's character served in the story, and the Melanie and Lindsay story.
Brian and Leda and Justin having sex in fic is something that (as you now know if you read this thread) squicks the fuck out of me, and I do think requires some deviation from canonical characterization to have happen, but if that's your thing, then I can only say what Michael said to Emmett about him and Ted: I wish you the best sex ever, I just don't want to see it. ;)