hey jeb,
brings back memories of my recent experience reading your thread. I had the very same problem on my brand new MK5. The top corner of the drivers door meeting the front wing seemed to tapper out and not line up with the profile of the car. It took the dealer 4 attempts to sort it out and on the final go, it looked good but they actually resprayed the door and wing!!!!
I rejected it because I told them I didn't want and paint work done.
I'm not driving a new replacement which isn't as bad but still has poor door alignment. Sadly I've come to accept this as all MK5 golfs as you say are hit and miss with the door alignment.