Yes, it leaves the radius. If you want to eliminate the radius as is done in American screw heads the tool post could be replaced with a Z axis milling attachment and the slot cut through or the slotting saw can be put in the mill and X or Y used to give the slot a flat bottom. I don't worry about it because with a 2 inch saw, the depth of the curve left on common gun screw size heads is only .0015 to .0025 in depth which is only barely noticeable and is of no concern with common gun screw drivers. Leaving the curve also gives a very clean, polished looking finish on the bottom of the slot.
Those tiny chucks don't have enough power to damage the threads. It's much like clamping a 2 inch x 4-1/2 TPI bolt in a common 6 inch lathe chuck. The square inch of the clamping area is so great the chuck jaws cannot deform the material.
@@RodHenricksonGunsmith I've just sacrificed a 3.5mm electrical steel screw by clamping it in a hand held drill with keyless chuck. With a magnifying glass there is visible flattening of the crest and measusing it shows over a thou reduction in dia. I call that damage even though the screw could still be used.