I had the same thing happen at the schmuck dealer when it was in for the 1,000 mile service. There was a small scratch/chip on the rear fender that I could tell was caused from the rear seat bolt when they were trying to install it. The last time, they scratched the outer primary, so I looked the bike over thoroughly before I took off. When I spotted the chip, I went ballistic.
They offered to have it fixed by a custom paint shop, and I told them they are welcome to try, but if it did not come out perfect, I wanted a new fender... period. It came back and it was totally perfect. Granted, the chip was only approx 1/8", but you can't tell it was ever there.
The nice thing about accepting it this way is, if they try to fix it, and it comes out crappy, at least you have something to use that looks a little better while you're waiting the many months for the new one. Worth considering.