Body matching headstock color

It inherently has edge lifting issues that are fraught with peril and finishing one side of a piece of wood and not the other will create moisture inbalances that can cause all sorts of issues down the road.

So the work is too labor intensive and risk that the neck will have problems in the future is increased. That's a recipe for Warmoth to avoid the practice.
Cant you get clear or amber on the back though, along with headstock color match?
You CAN get matching maple quilt/flame laminate on the headstock with matching dye job if you order at the same time as body. Not the cheapest option but it would get the result you want....
I think the guy means he wants just the headstock finished and the rest of the neck raw.  Like say I wanted a Canary neck with a dyed/finished quilted maple headstock but the back of the neck left raw.  That's what the guy asked, and no Warmoth won't do it.

edited because I'm retarded
I can see them not wanting to do it

One possibility is matte on the back, gloss on front.

Or... as was said, do your own on the headstock.  Its a bit harder with poly finishes, but with lacquer, all things are possible (and easily fixed too!~)