You should be able to set up your bass any way that you want. I don't see any reason why you wouldn't be able to lower your strings as long as your neck is straight.
I've got three Stingrays, and with a tweak on the truss rod I can lower my strings until they are almost touching the frets. I don't see the pickups being an issue, because they're fully adjustable too.
I think that before anyone can give you any useful advice at all, you'll need to find out the reason(s) that your luthier gave you. That said, I have a sneaky feeling that your luthier doesn't know what he's doing.
You may also want to contact Musicman's customer service—but you'll need to give them some solid information about exactly what's going on with your bass. They're super helpful, so they'll get you sorted out one way or another. http://www.music-man.com/contact-us/...tomer-service/