Musikraft says they won't install a nut on a neck they make because nuts and the string slots really need to be customized to each guitar once the neck is attached. Also, when you buy a Fender replacement neck, they don't fully cut the slots in the nut (presumably for the same reason). However, Warmoth will install a nut for you when you buy the guitar and I often hear guys at TDPRI talk about switching necks, buying used necks, etc. And I have seen posts where someone adds a shim to the connection between the neck and guitar to change the neck angle. I would think this would be the most likely thing to mess up the relation between the nut and the frets. I can see how the frets need to be installed before you can cut the string slots in the nut as fret heights differ, but how critical is it to wait to cut the nut slots until the neck is attached to the guitar?