CNC is used for all the big holes and cavities. Finish would clog up the small holes and would need to be redrilled anyway so its pointless to do these pre finish. CNC is used to get a body to shape and do the basic routing necessary that templates would of been used to do. Templates were not used for the small holes things like stopping the tuners from rotating, fitting the pick up rings, drilling through the cavities for the wiring and the output jack etc. After a CNC has been used to get the body and neck into the rough shape and carve, with all the cavities (pickups, electronics, trem) and any 'big' holes (6 tuners, tuner-o-matic post holes, pot/switch holes), the rest is totally done by hand. They have a jig made so that the output jack is drilled in exactly the same spot every time. Any small holes are not drilled because they would fill up with sawdust from all the hand sanding and clog up with the finish too so would still need to be hand drilled when the guitar ends up at 'assembly' - the people that fit the tuners, the pickups, etc would drill the holes needed for those screws.