Also the tailgate seams to be a common issue for alignment, I have seen three Mk6's all with similar poor alignment.
Funny, I've looked at my tailgate a few times and wondered if it was closed right on the left side I think. As I predominantly open and enter the boot from one side or the other though, I'd put it down to my imagination as I'd never compared both sides!
It pales into incomparison with the list of build faults I've found over the first six months though, the best being the front bumper expanding and popping out of its retaining clips on one side in the heat of the sun within 3 days of taking possession of the car!
I too have a raised pin-point bump in the paint, though mine is actually the same colour as the paint but is more noticeable as it's on the driver's side A pillar. I too took the advice to just leave be. It's hardly noticeable in reality and repairing it would likely just lead to something more noticeable!