depends on what kind of Nitro they are shooting. it absolutely can, but it's generally going to cost you a lot more money to have that kind of nitro sprayed.
To my knowledge that's what Fender Custom Shop uses. It's NOT what PRS or Production level Gibson uses. I can attest to PRS personally as my guitars had the typical ridiculous flakey PRS finish (despite being the new Nitro) that they refuse to take care of when there are issues. Only one of the guitars had the flaking though, and it's been sold a while ago with that disclosed.
Edit: Fwiw, I don't think Gibson custom shop is using a much different finish and this is part of the reason their relics often wind up looking hilarious. It's well documented their finish wears like older guitars pretty well--there was a miles-long thread on 'the other forum' a while back from a guy angry his aged guitar was starting to show new wear