When I ordered my Special last year, I sent the pickup to the factory that I wanted installed. I still paid for the pickup that was not installed and they didn't use, but knew that's what was going to happen going in. Like cmatthes said, if it's anything that they have to do differently than usual, they are going to charge for it.
I did get an ebony overlay on an unbound headstock without ordering or paying for it.... which is cool!