Well, I'm not going to argue because none of us really know 100% how they would do it, or if that's even the plan, just that my most trustworthy sources are talking about it
However, let's say that Universal was going to plan it...how would it work?
First, I don't think they'd have to tear down or re-arrange backstage areas...here's a pic I made of the 2 areas:
http://i660.photobucket.com/albums/uu329/techno9991/jawshp.jpg
As you can see, there's a single road that links the two and it's nearly a straight shot...it also seems relatively feasible that they could add a track between this road and the buildings next to it.
What about traffic? Well, like any cross-street or train crossing, there would be times where it would have to wait for a train car to pass by. If it ran, say every 20 minutes, it might not be so bad.
As far as theming the train ride, that's easy, just have screens on the train instead of windows looking out, projecting the ride over....similar to what Disney had planned to do with a Japan ride back in the early 1980's.
Ticketing. This is one where I am curious about it. Perhaps you can only ride the Hogwarts Express if you have your valid 2-park ticket. That would minimize the issues with having separate gates, etc.
Obviously we're dealing with completely uncharted territory and none of this may be happening. Just thinking about the logistics, it might not be as difficult as it seems at first?