What are your options? None, really unless you want to paint it yourself. Either the dealer will do it (if they do body work) or they'll farm it out to a local body shop. Either case, they have experience in doing this. They'll probably return it with a clean interior, or even if not, it can...
Rule number 1: when your manual says your vehicle holds X number of quarts, never drain the oil, change the filter and add X number of quarts. You can not assume that you drained 100% of the oil out. So, put in about 1/2 quart less than the X, then check it. If not indicating full, add some oil
I like the Hex Steps from DeeZee. I've had both kinds of assists on trucks and just prefer the steps over the flat bar or rail. https://www.deezee.com/product/hex-side-step/
They can easily add mud flaps at the dealership. Takes less than 30 minutes to add them to a vehicle. I usually toss that in as something I want (for free) before signing the papers. You must have had a doofus salesperson.
I had one on my F150. Worked well and no issues. Install was very straight forward. I kept it when I sold the F150, but I've just never installed it on my Ranger.
I had an older model Ranger do the exact same thing. The starter wouldn't work (could hear the solenoid click but starter wouldn't spin) when the truck was hot, but once cooled off, it started fine. Dealer replaced starter under warranty and no more problems.
Sounds like a dealer not being willing to deal with it and work with Ford to get it fixed. We bought a new 2020 Edge for my wife a couple weeks ago. When I went to wax it, I found the flat surfaces (roof and hood) felt like running your hand over sandpaper with little specks on the paint...