but what if the events of the comic are the backstory to the new movie, in much the same way that 'Countdown' supplied off-screen material for Trek '09?
Put simply, no. If IDW were to do a specific prequel for Trek XII like Countdown was for Trek XI, it would make the most marketing sense to release such a comic within six months of XII's release, just like Countdown was in fact within five months of XI's release. That way there it is a clear tie-in product with the movie.
While the ongoing has supposed hints about XII, it is not going to provide backstory for the movie. That is simply impractical and a bad marketing move.