Your Maintenance Minder
Join Date: Sep 2012
Location: Skokie, IL (next to Chicago)
Thanked 1,588 Times in 1,090 Posts
OK, the tail light "rub" issue is well known on these forums. The tail light assemblies have to fitted "just so" otherwise they will rub off the paint on the housing surrounding the tail lights. You can search for multiple threads on this- most have had good luck in the repairs and subsequent fitment, but there are a few here who thought the dealer screwed up the fix.
As for the other imperfections, those are clearly imperfections- either at the factory or by an unprofessional repair. The important thing is of course to first document this- which is what you did. Escalating this up to a regional representative, is, sadly, probably what will resolve the issue.
The second picture in your first post (is that the door sill?) is glaring. The others could be "rail rust" (Google this). There were a few members here who ended up with the regional rep at the body shop, where the body shop service writer went over everything and made it right.