VW pays for a complete fluid change with a Mechatronic replacement unit, which always includes the DSG filter. It is about a one hour job or less to change out the filter. You have to remove the air box w/ air filter, the battery tray and the battery, as well as some of the air ducts and the mass air flow sensor to replace the filter. The retail price of that filter is $39. I could see a $131 labor charge given what is involved.
In a nutshell, your dealer screwed you. I had my MU replaced at 27,000 miles on my VW CC Lux 2.0L. The replacement unit (which had to have its firmware flashed based on the VIN number) did come from Germany. Took two business days to arrive at the dealer, and 4 hours of labor to replace it. All under warranty. Dealer said DSG service does not have to be done until 67,000 miles. It will not have to be done at the 40,000 mile service.