I think the weight difference is about right. Mostly the difference between the basic and SL versions is aero-dynamic shape. The SL's have a "traditional frame" shape (all standard "round" tubes), while the standard have the seatpost flare around the rear wheel, and some differences in the rest of the frame.
I read an article on thepaceline.com about how the team will all ride Madone 5.9's (even lance) on the "flatter" stages, and then the climbers like Azevedo and Lance will switch to the SL's on mountain stages. They'll also switch from aero wheels to the really light carbon ones.