Well, I discovered rust on my offside rear arch a few months ago.
Took it to my nearest dealer (sadly) and eventually VW confirmed it would be repaired under warranty. So I left it in then collected a couple of days later. The finish was crap- runs, thin lacquer, imperfections etc. So it was left back to them reluctantly to give them a second chance. Then when I picked the car up all appeared to be well. However when I got home I noticed the orange peel effect is quite obviously different and there are FAR less metallic flakes (diamond black) than the drivers door.
I wrote a letter to VW and they basically told me my problem is with the dealer, despite it being a VW warranty. So now I'm left with a poor finish and I'm understandably refusing to give the dealer a 3rd attempt.
In short, if there are no stone chips it should be covered, but chose your dealer wisely...