Well, let's summarize:
1. Everything is fine
2. "Guarantee they beat your car..."
3. Should have been flat-bedded to your dealership
4. Everything is fine (again)
Reality: NOBODY here has ANY idea how it was driven from Dealer A to Dealer B.
Reality #2: It probably doesn't matter one iota
Just follow the normal break-in procedure instructions and enjoy the car. Or lose sleep over it every night for the next 5 years, waiting for it to blow up prematurely. I'd go with the first option. Congrats on the new car!
Bingo. Don't sweat it, you have plenty of warranty time for issues to surface and get resolved.