Glad you got yours sorted out OK, you expect it to stay fixed or will it just keep recurring?
I expect it to happen again but on the drivers side this time, only because I'd have to pay for it then! While I appreciate the dealer fixing the first one free, it's a production repaint where they panel blended into the roof and passenger door. Just enough orange peel to see when sighting the car that drives me crazy. I have the stuff to supposedly fix it but I haven't gotten up the bravery. I paid for a reshoot once when I wet sanded through a quarter one time, that'll make you gunshy.
Funny story: I bought parts off Craigslist and when I met the guy and he was driving a car identical to mine. We got talking about the rust and said he didn't think he had any, and asked where to look. Sure enough his was perforated through in the exact same spot in the pass quarter.