Thing is, you gotta assume the dealer filled the sump up to the top dipstick mark when you bought the car... Unless you know for sure, then you're not really sure *how* much oil has been used.
I wouldn't think 2mm over the top would cause harm.... 2cms yes!
Now that you've topped up, do another 3.5K and see how it goes (although that may take you pass the next service date, unless you're on long-life services?)
I read a VW Driver mag a few years ago and it stated that a more aggressive regime for running-in is preferable to a gently gently touch as the bores never seem to achieve the slight lip at the top that helps in oil control, Now I'm sure they don't mean rag the ar$e of your pride and joy, but lets say, a quicker acceleration up to cruising speed etc.
If your at all worried, bring it to the dealers attention so that in a years time and it's still losing oil, they don't fob you off.
Can't remember exactly, but IIRC official figures are 1ltr for 10k mls is still within limits!! Should say in the manual....