It will work. Tommy has his own forum and many members over there have done just what you are asking about. Also, keep an eye on the USACG site, because occasionally there are web specials (I got an alder strat body for $95 a year ago).
When you call in your neck order, tell Tommy its for a Warmoth body and see if there's anything he feels needs to be done to adapt. There probably isn't.
Xeromus, I agree with you on their necks, they rock. I've got two of their necks and two of their bodies. I also prefer USA CG bodies for Strats and tele's because I can call and ask Tommy for exactly what I want tonally, and he delivers. On my first strat body I ordered, we talked about the tone I wanted and he called me back 30 minutes later very excited and said he found the perfect piece of alder for me. He delivered on the tone I was looking for. He's a great guy and knows what he's doing (not that the Warmoth folks don't also).