When I look on the Trek website, I do not see what you describe. The two Madone 5.2s, regular and pro, and the the two Madone 5.5s, regular and pro, have RaceLite wheels. Perhaps you are looking at the RaceXLite tires and not the wheels in the pictures?
I very seriously doubt you will be able to find a shop that would mistakenly throw the RaceXLite wheels on a 5.2 without charging you. If you want the RaceXLite wheels, however, just offer to pay the price difference at retail between the RaceLites and RaceXLites and the shop will likely make the substitution for you.