I am going to disagree with you, it will not void the warranty. It is an OEM tranny, they might not fix that transmission if something failed, but the rest of the car should still be covered. I am pretty sure the dealership wouldn't notice that the car should have a 5 speed, considering a lot of VW's come with a 6 speed.

And to answer the question, it isn't that hard of a swap. I wouldn't ask the dealership to do it though, unless you have some serious money to blow. You can find used 6-speeds on vortex, just find someone to put it in, or do it yourself.