I agree! The new owner would be a fool to alter this guitar.
As far as the nut, a guitar shop can custom cut a nut from a blank:
I've been reading different reports on line about the price paid for this guitar. Evidently his bid was about 500K, so the additional money must have been the auction house's "buyer's premium"... a rip-off fee charged by auction houses to the Buyer... for absolutely no justifiable reason, as far as I can see. The auction house is already getting their 20% (from the seller), so what's the Premium (from the buyer) for? They all do it, and they all get away with it. So the House takes 20% from the seller, AND charges 15% to the buyer... for the privilege of buying from them.

In that scenario the House is getting 35%.
If I were Selling this guitar I would not sell through an auction house. The buyer's premium inhibits bidding. Bidders figure the BP into their bids, so the high bid is not as high as it might otherwise be.
This Page explains the buyer's premium pretty well.