That's the shitty thing about painting a car with paint already on it, you never know what's underneath or how good the person was that did it..Originally when it was painted last year, they stripped the trunk lid and header panel to bare metal as thats all they recommended it needed.
I had issues arise on the hood since then and when I brought the car back they recommending stripping down to the bare metal, and applying some sealant before repainting. The sanding to bare metal and repaint was on his dime, the only thing I was going to pay for was the sealant. Well after stripping it down to bare metal they found the flash rust all over the place. Hard to get pics of it, but I saw it first hand and it was like cancer, it was fucking everywhere. The new hood that I bought looked really good, we had that one blasted and when it came back from the blaster it was worse than my original hood, like way worse. That shit was all in the nooks and crannies.
As mentioned, this flash rust shit is foreign to me. I asked a buddy of mine who owns a body shop in the city. He also said if its as bad as I described the hood is fucked. I'm not even remotely thinking he is trying to fuck me in any way, shape, or form. He has stood behind his work and the other issues are 100% on his dime no questions asked.
Any unprepared steel panel will instantly start to rust if it's not treated or coated with something to prevent the air from chemically turning the steel to rust. Metal that has pits in it can still be saved and have a good long lasting paint applied over it. It just takes all the necessary prep work such as treating or removing active rust. Then sealing it in a epoxy. If you look at all the pics and videos of my nova 90% of it sat in bare steel for a few years. Lots of areas where flash rust started to happen. I mechanically removed as much rust as possible and then did a rust neutralizer or converter, clean, prep and now it's sitting in epoxy. I don't expect to see any rust pop back unless I didn't do something right.
I'm not nitpicking, but unless the metal is deteriorated to where it's thinner than it needs to be. I would think your painters should be able to stop the rust in its tracks, seal it up with epoxy and body work over it and you or anyone else should never know what the metal underneath looks like. Just trying to help you out without having to spend a crap ton of money on patching two hoods together and all the bodywork that will be needed.