I built Ben's guitar and the way I did it was to get a standard neck cut for a Fender style nut. I then routed off part of the reverse curve where the fingerboard joins the headstock. This gives about .5 cm between the nut and the locking nut. Ben has screw in lock nuts not bolt on, however that shouldn't make a difference. On the neck we were using (a Warmoth), the truss rod adjuster is on the bottom of the neck and also on the lower side at the heel.
Thanks PhilKing! Actually I'm interested in a neck through custom guitar so I guess the truss rod adjustment would be on headstock?
I hope it's easy for a luthier to build the neck a few mms longer after the nut so I don't have to put anything on headstock. It won't affect the scale once it's after the nut I guess.