I would just deal with it. You've already waited a long time to get your bike, and like you said, its barely noticeable. If he/she got major things wrong like wrong lengths, angles, questionable welds or brazing, then I would probably get a replacement frame.
I was told that custom frame builders strive for a 1-3mm tolerance and most major manufacturers have a 5-10mm tolerance. My framebuilder also said he's seen a Colnago that was off by 15mm.