Musikraft all day, every day, over Warmoth.
Can't stand Warmoth. Too much show and not enough go. High prices. Unwillingness to do very simple custom requests. Mediocre fretwork. In most cases, a neck "style" locks you in to certain options, which cannot be changed. E.g. You can't choose the radius (or can't choose certain radii), nut width, or truss rod adjustment style on most of their necks. Those things are the meat and potatoes of a custom neck; they're the things that need to be able to be spec'd to make the order worthwhile.
Musikraft has way more of the options that actually matter, and their fretwork is superior, IME. Warmoth has only a handful of neck profiles. Musikraft has dozens, if not scores. You can choose your nut width, profile, radius, and truss rod type on most of their neck styles. You can get a vintage-correct Round-Lam ("veneer") board there. And MK don't front like they are this amazing "custom" shop, and then turn around every single time and tell you they can't do a simple mod.
Warmoth is the place if you want flashy woods and a wide selection of cheesy inlays. For most anything else, there are better options. They used to be the real deal, back in their old days, but they have become so middle-of-the-road since then, that I almost consider them the Guitar Center of made-to-order necks and bodies.