Yes, I think you are right. That option seems to apply only to realtracks, not to usertracks.
I surrender.
I'm starting to think that there's no way to tell BIAB not to transpose usertracks.
I will add this to the wishlist. It's probably a very simple option to add, and I REALLY REALLY hope it will be implemented soon. I think it's quite important. I'll try to explain why in the wishlist forum.