That's not poor QC, someone just removed the screws from the car. Can see the shiny metal where the screws tightened. Should send a complaint to proton hq. Somebody in the warehouse or transport section is stealing metal parts from new cars.

I don't know if the scratch is related to the door fitting. I believe if the factory would have fix any bad fitting issue and reworked any big scratch before release to distribution. Please check the door to see if there any part of the door hitting the area. Check also the 2 remaining screws for signs of missing paint. If so then I think the door was removed for repairs and reinstall back. This could be a reason for the scratch and they must have lost the screw. Better complaint loudly to the branch manager and the proton hq.