I have an '05 Pilot 2.1, and it's all 105...the specs on the dealer's website may be a carry-over from last year, or something. I would definitely bring it up with your LBS, make sure that if you're paying the '06 price, you get the better components.

Wisconsin, per the Trek archives, your '05 should have had Dura-ace in the rear. The '06 has all Ultegra, but the MSRP is $100-200 less than last year (WSD price is higher?). That said, if you got a great deal on it, then it may not be worth the trouble of taking it back in.