The FR nut needs the shelf cut to work properly, else your strings will be way-super-high off the fretboard. If you're buying an unfretted fingerboard, I'm assuming that you're going to be building your own neck. If this is the case, you can very easily plan your neck construction to accomidate for the shelf. You'd need to find the nut dimensions, fingerboard thickness, fret height, and everything, and draw your plan out full-scale, and you should have no problems. Don't quote me on this, but I don't think that you need to have the nut mounted on the fingerboard wood, if that's what you're asking.
I would look up more information regarding FR systems with a compound-radius fretboard, to make sure they're compatible. Also, unless you want that particular scale length, I might go with a Gibson-style fretboard, so you don't need to risk cutting the fretboard before installing the nut. Not that it'd be a particularly tough job to do, just that accidents happen.
Not to dissuade you from building your own neck, but I know from experience that Carvin makes very good necks. I don't know what your estimated price range is for buying a neck, but a Carvin bolt-on with a FR shelf is $185. And, of course, any options they list on the guitars can be applied to the replacement necks.
Hope I helped some.