Daryl,
For German custom guns,at least, they are usually cut with a jewelers saw.When they are "clocking"or "timing"the screws, they turn in a screw with a temporary slot in an extra thick head.Then they mark the location of a new slot"fore and aft",and saw or file the new slot to depth and file the head to the necessary thickness(thereby removing the old slot).Of course they could cut the new slot in the milling machine with a slitting saw, but the set up would take up a lot more time than doing it by hand.
Mike