You can order a floor shop custom through several members (who are SD dealers) here on the forum.
As others have said, you will have to get the pickup with the cover loosely attached. You'll pay about the same as if you ordered a covered version of the same pup, but you'll probably have to wait for a few weeks as it is a semi-custom order.
There are several reputable dealers here who would more than happy to help you out:
MartinSixStringCustoms
Wymore Guitars
Lewguitar
Sorry if I missed any other dealers. I was unsuccessful with my search! Shoot any of them a PM and they'll hook you up.