To the OP, I understand as I have a similar OCD tendency. I noticed upon receipt of my rMBP a slight scratch/indentation on my rMBP's plastic hinge/clutch cover. It must have been like this from the factory as the area around it, and the computer as a whole, is in perfect/like new/immaculate condition and must be attributed to the manufacturing process.
If I was given the opportunity to return/exchange it for a new one, I would. It would irritate me knowing that this imperfection wasn't caused by me and my philosophy on buying new is that it should be near immaculate with anything happening afterwards on you.
OP, it really depends on how you feel and if it will be much of a bother on your mind in the future. Many won't care but for some people like me, such a thing will be a bother for a long time till I replace it... with a tMBP. That won't be for a few years and thankfully the scratch is somewhere obscure.