Put it this way: even Warmoth won't color match headstocks to finished bodies, and they're some top-end finishing folks.
That said, a well-equipped paint store will have a color-matching computer that can scan an existing finish, then scan the raw material you want to finish and generate a recipe for a finish to match and mix it up for you. In some cases, you can even be finishing different types of wood and get remarkably good results. I've done it with stain for cabinet/furniture finishes.
For a headstock, I don't know why Warmoth balks. It's far enough away from the body that I doubt a small difference in shade would be noticeable. But, who knows? Maybe they mix colors by the seat of their pants, or have had too much experience with anal-retentive types bitching to the point where they just said to hell with it. They'll still do it, but they tell you up front it may not match and won't make any guarantees.
I don't know if I'd want to do it away from home, but that's just me. I like to stay on top of the process, which can take some time. It's kinda like combat - lotsa waiting around interspersed with short periods of sheer terror, and if you're off your game you can fail spectacularly.
If it was me, and I hadn't bought the neck already, I think I'd trust Warmoth to get it close enough for rock'n'roll. For what they charge and the amount of work it is to do it yourself, you may be better off. But, if you want to bury a decal in the finish, they definitely won't do that. It is written. So, that's a consideration.
