I would assume that they could rout an F-hole because its a semi hollow body. Im not really sure about the double F-hole option, but I bet if you could call they would do just about anything for a price.
Some of the chambered bodies like the Tele, Strat, and maybe LP have an F-hole route already. The laminate top may or may not be cut to reveal it. I imagine it would be much harder to reveal it after it is taken off of the CNC. A thinline however is all open, so cutting it into the cap, the tolerances wouldn't have to be on a gnat's ass.