I bought some touch up from the dealer for some minor rock chips, matched well enough that unless you get close and sit and seriously search, you cannot tell there were ever any chips. A large scratch may not be hidden as well, but if it don't, it's not like you couldn't then have a body shop fix it. Unless it's a show bike (ie trailer queen) a few scrapes and scratches are to be expected if you actually ride it, I agree, it's now broke in, and unless your trying to sell it, don't worry about it, bags are plastic, they wont rust.
"Be Water, My Friend" Bruce Lee 1971
2013 CCT Grasshopper Drivers Backrest, PVC Self Made 1/4 turn Throttle Ring, Thrush Self Modded Mufflers, Kuryakyn 4526 Tour-Tech Adjustable Cruise Mount/Tour-Tech Pegs