I had this issue come up on an 05. To get the 05 the dealer had to have a purchaser. In this case they had their service manager put his name on the deposit. The bike was new as in it had never been riden, but when they sold the bike to a real person they found out the warrantee had been running and they only had 9 months on the original year.
The dealer was not trying to cheat anyone. The resolve on this was for the dealer to deliver the extended yes warrantee for a lesser cost.
Everyone was ok with the result.
Work intelligently with your dealer to see what they can do either with Yamaha or on the extended warrantee.
Don't let it impact the quality of your ride.
This is a completely different situation. If you got a new 2005 without pre-ordering it, you were not following Yamaha's rules. The dealer was also not following the rules by ordering the bike without a buyer. There is *** for tat here. You got a bike without having to put down a deposit and waiting several months. The dealer, by not following the rules was actually doing you a favor by having a bike for you. Your option, if you didn't like that the warranty had already started was to wait until the next model year and order a bike under the pre-order program.
It is a completely different situation when there is no pre-order deal, and the dealer sells a bike as brand new in the crate, and then the customer finds out the warranty already started.