Update:
So I took the car in and politely showed them the defects and they immediately agreed that it had to be fixed under warranty. I asked them about the clearcoat burn on the sail panel and they said it would not make sense to burn it there because a tape line would eventually show up, so they would have to re-clear the whole panel.
They paid for a rental for me and everything so I suppose I am a happy camper in this warranty claim.