That gap varies wildly on every mk5 and mk6 i have seen.
As i have looked at over 200 of them now and im not joking, as i thought mine had a paint issue in that join but it seemed there all like mine but i kept checking as needed reasurance

Some that gap is small some like mine its wide. It seems to vary even on the same car from side to side, its normal im, after seeing so many.
Its something most people would not have ever looked at unless there was a problem like you have now.