Baldy,
The spot weld drill (or cutter) just cuts through the top layer of metal if you do it right. If properly centered on the spot weld, it basically removes all the welded material and then nothing is left holding the two pieces of metal together.
Weld stainless with stainless rod/wire or with a TIG welder with stainless filler if required. Grind/polish the weld smooth and there will be no discoloration - it is "stainless"
