Like others have said, take the $400. Yeah, it sucks, but $400 is a pretty good offer for two drilled holes.
That being said, my salesperson showed me my folder for my order, and across the front was written "DO NOT INSTALL FRONT LICENSE PLATE FRAME!!!" and if someone didn't notice that, then I don't know what to say.
My dealer did it as well after two emails and a text asking them not to, but then went back and touched it up. Ordinarily there are two small indents from the factory. Someone apparently drilled out the holes and the then touched them up, being as the bag that has the factory license plate holder in it isn't open.
I could tell that my dealership would have been ok if I walked, so I wasn't going to let this be a deal breaker.
It's annoying, but not as annoying as I figured it was going to be. High probability I'll cover that area with a decal anyways.
I told my dealer not to and they did the same. When I got there the plates weren't mounted, but the holes had been drilled. I imagine the set up guy did his thing then the salesman noticed and took it off. The holes aren't noticeable unless you know what you're looking for.