The screws were likely made with thick heads and a temporary slot. When the gun was being "fit up", the screws were pulled up tight and the permanent slots marked to all be "fore and aft"( clocked or regulated). The screws then had the permanent slots sawed or filed deeper to the finished depth. Finally, the screw heads were filed and polished "flush" to the surface. When the surface was rounded or tapered, the screw head wound up thicker on one side than the other. This is especially noticeable with wood screws holding the trigger guard. When such a screw is turned out, one side appears to rise and the other appears to sink below the surface; but when it is turned back in to the proper depth, it is flush again.
Mike