So got a little sideswiped the other day looking for recommendations plastic filler and or ideas for the whole project, paint or go with something else?
One of (the many) ways I have "repaired" such scrapes was to rough sand (80 grit, IIRC) the panniers and then paint them with flat black spray-on paint. Now, I'm using stickers.
Once inside the pannier, look for any stress cracks to the mounting bosses for the latches. It would be prudent to reinforce said mounting bosses with JB Weld or similar to prevent future issues.
You might want to look at Plasti Dip paint. Some on this Forum have used it successfully to paint over the graying black paint on the NT. It might also help fill in some of the light gouges and scratches. I am not sure if they have a silver color that is close match or not.