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If it's not bad or that noticeable, I'd leave it alone and NOT fix it. There's nothing worse than a door with a different shade of the color from a body shop repair, especially silvers and reds. There's nothing like a factory finish, so just ask yourself if you can live with the blemish, maybe ask for compensation like free oil changes????? My VW heated mirrors didn't work from the factory and I negotiated a timing belt change no charge so my dash wouldn't have to come out.
If you decide that you are taking the truck I'd expect an additional discount. This will probably be on any report pulled for the truck for the rest of it's life.
My wife was test driving an f150 a year or so back. A deer ran into the side of the truck while she was driving it. The dealers insurance covered the loss ($9000+). They offered us the truck for an additional 10% off sticker after the repair was done. They said there would be a crash report on the truck. Not sure how it would work with this situation.
I doubt you'll get 10% but it should be worth something IMHO
My driver's side rear door has a small crease in it, right at the body line under the window. It is unnoticeable if you look straight at the door but if you sight down the body line it sticks out. My wife noticed it about a week after we got it and was like I'm showing you this so you don't freak out when you hand wash it (not that I would ever do a think like that). It was a flaw in the door before it was painted as there isn't a mark in the paint and the finish is smooth. I decided it was something I could live with and didn't say anything as it would just be a PITA to fix especially with the door being aluminum.
As others have said, you can either live with it and get some kind of deal, have it fixed or wait on a new one with just as much chance of something happening again. My family has had the worst experiences with ordered trucks that I will never do it again, somebody always has one close enough to meet my needs, the truck I now have is a prime example.
I know it's difficult waiting on your new rig. But if it was me, I would not accept it without the dealer giving you a substantial discount. If they decline.... look for another one or place a new order. Just my .02
Sometimes it is a simple matter of wet sanding and polishing the door, I would go and look at it yourself and see what it actually looks like, then ask what kind of repair it will need.