Sure thing!
Nitro finishes are currently only available on Custom Shop instruments. It's a $572 MSRP upcharge which turns into $400 added to the advertised price of an instrument. Both the body and the neck finish are included in that one charge.
If you'd asked me a few weeks ago how crazy they would be willing to get with electronics in the Custom Shop, I'd have said "not very". However, in the past two weeks I've had someone ask if they could do a JB with the 70's bridge pickup location. G&L said yes, and it's a small upcharge. Then someone else asked if they'd make a JB with L-2000 pickups in the L-2000 locations but wired like a JB (so passive vol/vol/tone). I was gobsmacked when G&L also agreed to do that, and for the same small upcharge.
It probably still needs to be handled on a case by case basis, but I've learned that it doesn't hurt to ask!