I'm guessing........... Ford, in an attempt to streamline things, has the opinion that serious buyers will get the manual transmission and therefore offer performance options such as the brake package and choice of gear. These are not options on the automatic. Both of these options require different tunes and testing (the gear is a quick change, but still requires some amount of testing). Since the automatic is geared differently from the manual and the brake package has a custom ECS tune, Ford doesn't have to mess with it. In other words, the automatic comes as is, end of discussion.
2006 GT, FRPP drag pack, FRPP handling pack
2011 GT ordered 1/30, off the truck on 6/21
Black GT - 401a, Black/Cashmere interior
6 spd, spoiler delete, security package
3.73, HID, comfort package
Brembo brake package, Glass top
First mod - CS front fascia