I had a rattle from day one, knew I should have gotten a 3 door 
If I use my elbow to press on the top of the rear door card it would stop. The car is going into the dealers in a couple of weeks and I have so many problems that they booked it in for minimum of a week. So much for VW being well built.
I'd personally strongly advise against letting a dealer chase down relatively minor issues like interior rattles. Any rattles for that matter. Ask yourself how much it's really bothering you first. And leaving it with them for a week?! Madness. The car will come back with one problem fixed and 3 more created.
As for 3 versus 5 door... the rear panels / door cards are much easier to remove on a 5 door 
The reason it is going in for a week is all the other problems.
Various rattles
Extremely unstable under hard braking
The discover nav unit needs replacing
Rattling/nocking rear suspension
Both keys only work 70/80% of the time after replacing batteries
The 'should have gotten a 3 door' comment was a bit tongue in cheek.