Well brother, join the club! I doubt if the dealer will address that issue of re-painting, but... there is a bulletin out about the black rubber seal that the top sits on. The new one is slightly crowned. Which raises the top enough to clear the body. Also you can adjust the top, which I assume you have already done. When you can slip a business card under the top at the point of contact with the seal, then the adjustment is correct.
"Cleartastic" makes an item that you can apply to protect that area, but if you are still under warranty, I would dump it on the dealer to fix! Good luck.