My local dealer has a Mustang on it's showroom floor with a sticker price of $86K. Please don't get me wrong as I love my car and I love Mustangs in general, but there is no way I would pay $86K for any kind of Mustang off the showroom floor.
Undoubtedly, CAFE requirements are affecting the number of these higher performance special editions planned. The Shelby GT is strapped with the Guzzler tax and its mileage is pretty close to the standard GT as I recall. Ford probably knows that if they manufacturered a much larger number of the higher performance Stangs (Boss, Bullit) they would sell them all since "market adjustments" would not exist. Ford would make more money, but there are too many low mileage vehicles in their line-up and they just don't sell enough higher mileage vehicles to balance it out CAFE-wise.
Works great for Ford to put out a few higher performance stangs. Dealers are happy as a lark with the high mark-ups. Individuals unable or unwilling to pay inflated SE prices can go build their own with Ford Racing aftermarket components purchases (profit for Ford) and assume risk for repair work for the modified cars (money ford saves), and the CAFE requirements are not affected. And of course they sell more standard GT's to be modified
Basically, the SE Stangs to me serve Ford as marketing devices. They are better off just selling a few to inspire the masses and to keep interest in the Stang overall.
You are absolutely correct. Unfortunately they let their dealers get away with the same stuff when the new T-Bird came out, and they either didn't learn or chose to ignore the lesson from that experience.