I gotta do some searching but it was explained to me that at the factory they would run the engines extremely lean... like to the point they had to add additional cooling. Then when the bikes arrived at the dealer they would reflash the ECU and have it normally tuned again.

EDIT: Not exactly that... from another user "They admit that the modified bikes bypass emissions requirements, whereas the unmodified VWs didn't meet the requirements and had to cheat to pass inspection."