That is strange...looks almost like they wanted to pry up that window to reach around and unlock the door.

Either that or a BB gun shot.

As for repair, I would recomend that you make sure the surface is very dry and there is no surface rust forming. To assure yourself about the rust, go by some naval jelly or rust killing acid (several types at pep boys, auto zone, etc), and apply it to the bare metal, then wipe off.

Follow that with your touch up paint immediately after so that there isn't time for the surface to oxidize even the smallest amount.

Touch-up paint never looks quite right though, and unfortunately you will always see those spots. It may be worth it to you to claim it and have the insurance repair it. To do it correctly, they will likely have to paint the scratched areas, with a little bit of blending into the current 'good' areas, then re-clear the whole rear 1/4 panel, sail panel and door. I believe they will be able to match it close enough to where they wont have to mess with the roof...and there is a 'gutter' where they should be able to hide a paint line.

SQ