It's gas mileage. That's why the track pack only comes with 3.73:1 gears, too.
If you ask Ford Racing, then they will recommend the FRPP drag pack, which comes with 4.10:1 gears for the manual and 3.73:1 gears for an auto for approximately the same final drive ratio.
The track pack is around to make the Mustang GT more attractive until the new engines come out next year. Auto makers use this ploy all the time.
Ford could offer a similiar option on an auto. They did just that with the Shelby GT.
Why not? It's a good profit margin.
Gas mileage again. You want to keep the enthusiasts happy, that means at least a manual transmission. On the other hand, for CAFE reasons, you want to keep your mileage numbers up. The track pack is small number of sales. It won't hurt CAFE too badly.
Take it one step further. Why don't they offer a GT500 in an auto? The Camaro SS, G8 GXP, CTS-V and Corvette all have automatics. The Corvette auto has been outselling the Corvette manual for decades, at least since the 70's, I believe. GM makes money on performance autos. Why not Ford?
GM works hard to get all of those auto cars decent gas mileage for CAFE. That costs money.
(Why no independent rear suspenions for the car? That costs money, too!)
The average person shopping for a Mustang auto has traditionally been happy with the performance level offered. Mustang owners accept the highest performing models won't have an automatic option (no excuse in this day and age, though). Under this model the track pack and the highest performing Mustangs (like the Cobra) will be limited in production (enthuiasts still happy, development costs lower), while most opt for the standard GT or V6 models (better for CAFE).
The only time Ford releases a "special" Mustang with an auto is when at least two conditions are met:
1) Limited Production from the beginning and not just an option block anyone can check on a GT.
2) To keep interest up. The Shelby GT was designed to keep the car interesting after the first year of production when sales usually take a slide. It road a wave of popularity. Mach 1 autos were produced to keep the car fresh until the '05 model came out. Offering an auto meant more Mach 1 sales, but since the production totals were carefully controlled, Ford didn't have to worry about it hurting CAFE as much.
__________________ 2006 Mustang GT, Automatic
93 Bama Chips Tune/3.73 gears/Steed CAI
NOS Single Port Wet Nitrous Kit (75 shot)
Steeda LCA/Eibach Sway Bars/Spohn Panhard Bar/Steeda Panhard Bar Brace
FRPP "Stinger" Axle Back Exhaust/BBK Shorty Headers
19 lbs OZ racing wheels w/ 255/45R18 tires
Daily Driver: 2009 Pontiac G8 GT | 
