I had these same issues. Dealership wanted $3500 for all my issues (I had a few others).

I don't care how my car looks, so I got some bondo, automotive spray paint, and sealer and fixed the holes myself (after sanding the rust away in the first place).

They also got me for a small rust hole in my muffler. I ended buying a new one from Oriellys and installed it myself.

Saved tons of money doing the work, and a bunch of other things myself.

Also, anyone who said the dime sized hole in the runner board under my rear passenger door is a safety hazard GO FUCK YOURSELF YOU TWIT.