I don't expect anyone has actually done that yet - since the guitars are not yet publicly available.
But I do recall reading somewhere in the official product information that it is designed so that the mag pickups can be replaced without affecting the integrity of the system. So presumably the answer is yes - it can be done. However, a cautious person might wait a while to hear the results of the transplant experiments of the less cautious. Are you a leading-edge or bleeding-edge type of person?
I didn't realize that nobody has received their JTVs yet! I knew they were available for ordering but I thought that there was an initial manufacturing run (aside from the prototypes and betas) that was sold to the lucky few who placed advanced orders and that the rest of us were now waiting for our shipment to come in. Drat!
Um, yeah, I am sort of a bleeding edge sort of guy, which at times I do regret. I guess I'll play the JTV out of the box for a few weeks before I take it in and have the Sustainiac put into it. But if I'm not completely thrilled with the other pickups or the tremolo system, they'll have to be replaced.
I just heard about RackVax (www.rackvax.com) and I'm very interested in them as well. Does anyone know if they are a division of Line 6 or are otherwise affiliated with Line 6? I've got a ton of questions about them as well, but perhaps there's a different forum where questions about RackVax vs. JTV would be more appropriate?