I wouldn't worry about it as the minor amount of cupping really isn't hurting anything. It's basically a result of the media tumbling process Savage does to them to knock off the sharp edges (something PT&G doesn't do and as a result you have to file the edges of the lugs to keep them from catching and hanging up on the receiver when working the bolt). Also, the PT&G bolt heads have left a LOT to be desired in terms of fitment. Kiff's an exceptional machinist and a tool maker, but he's no gun guru and knows little to nothing about Savage's to know what he can and can't get away with as far as tolerances to ensure his parts will work in all the variations of Savage's made over the years.

That said, if you're that worried about the cupping on the bolt face just have a local machinist or gunsmith chuck it up in the lathe and take off just enough material to square it up. You'll need to check and possibly reset the headspace after doing so though, but you'd have to do that if you swap to a PT&G bolt head as well.