Hi,
You are not alone with this problem. I just got my 2005 Trek Pilot 5.0 two weeks ago and it came with Ultegra on the rear instead of Dura Ace. I asked when I picked it up and he showed me a catalog that said Ultegra, but I wasn't sure if that was an 06'. I haven't changed it out as the dealer just said bring it in but didn't say they would do anything. I got a great deal on it but feel I should contact Trek some how. In your case I would definately look at other dealers to see if you can get Ultegra at same price etc. just in case your dealer doesn't want to give you the Ultegra. I couldn't really do this as the 05's were sold out now. I would definately try to get the Ultegra as it is much better. I do love the Pilot and you will too!!
Good Luck,
Wisconsin