Okay I had exactly the same issue up until I had my car sprayed.
Since the paintwork over the rear arch was done I no longer see a difference between the arch and flap.
From this I summize, the car whilst originally being painted does not include the filler cap. The cap I presume is done elsewhere within Nissan, maybe a different booth, different layers of paint I don't know.
All I can say is my car no longer contains this problem, so its got to do with Nissan not spraying the entire car with the cap on. If you think about it, the cap wouldn't be installed when being originally sprayed and only installed later in the process.
Well that's what I think anyway and would seem to add up.