I don't think it's too terrible, to be honest. The speed knobs are an eyesore, but easy to change, and it's easy to get a new (or even vintage) scratchplate and change it back to two pickups. Ok, so there's a bit of wood routed out under the plate.
It's only a "Rare Valuable Vintage Medallion Flying V" with the benefit of hindsight. The owner might've added that third pickup in 1974. I wouldn't hesitate to buy a new Gibson and modify it.... and I don't think you would either.