Aftermarket tunes will provide similar increases in horsepower, torque, throttle response, and overall performance to manual and automatic Mustangs.
The perceived difference in gains comes from the difference in the way that the transmission computer is calibrated for shift times and duration.
However, this can typically be compensated for with a little practice on timing your manual shifts when driving.
The bottom line:
Manual and automatic Mustang owners can expect to enjoy the same high-performance benefits from applying an aftermarket tune to their vehicle.