My dad-in-law is a machinist and his solution (which I thought was extravagant) was to make custom presta valve stem screws. He'd machine start with round bar stock, machine a smaller lip just a 1/2 mm high, that would fit inside the schrader hole but not exceed the thickness of the rim, then cut off the bar stock about 5mm above the recessed lip; drill and tap the center hole, then mill off flat on 6 sides at 60 deg. rotational intervals. Lots of labour for a small part, but in quantity, these could be cast instead of machined for pennies I think and bundled with standard presta tubes. Flip it to the flat end for normal rims. Turn it around for schrader holes. It would nicely center the stem in the hole and provide relief without cutting the tube at the base of the stem.