warmoth is a replacement parts company, not a custom shop. and the hollow thing is definately not something they are willing to do. sorry
they can cut custom body shapes and headstock shapes if you supply drawings but i dought they will incorperate any kind of hollow option in a custom shape body.
the reason is that they may have some skilled workers but they are not luthiers, the custom stuff is cut by hand, that's right no cnc if you supply drawings.
doing a hollow body with a router would be a pain, the builder would have to be mindfull of a back contour if that was ordered, also there would need to be bracing under the top, a thinline has solid wood between the neck and bridge, just the wings are hollow and the top is thick, a warmoth hollow is really chambered like a thinline but has several smaller chambers. they don't have a set design for a true hollow body. maybe someday in the future they will develope something, but warmoth doesn't seem to want to risk the potenital problems doing certain things as one off.
i know as well as you that the right programmer could do it as fast as anyone with a band saw and router but that's just how they do it. gregg mentioned looking for a programmer so they may not have one right now, who knows.