Yes, if you leave it as square piece of wood, it's a lot easier to line up and get straight when you clamp the pieces together (when you make the scarf). If you have a cut headstock (especially if you do asymmetrical heads like I do) and you try to mate it up to the neck and clamp it, it might look just fine up close when you line it up but when you step away you'll realize that it bends off in one direction. If you clamp two square pieces together it's a lot easier to see that everything is straight because you can just lay a straight edge across it after you put the clamps on.
Brett Morgan said:
Josh is there any reason why you wouldn't shape the headstock before you make the scarf joint? It would seem that it would sit better being flat.