From what I understand, in transverse applications, the 6F55 transmission is limited to a lower torque capacity (350ft-lbs). Whereas, In longitudinal applications, the 6R80 transmission can support a greater amount of torque. Therefore they tune the engine accordingly.
Also a neat thing worth mentioning: The 6F transmission series was co-developed with GM and is used in many GM vehicles, under the "6T" nomenclature.
^^^What they said Tim. My understanding is that the other part of this is that Ford did the additional tuning on the EB for the F-150 in order to get the torque numbers up both for towing and for advertising. They definitely wanted it to have higher torque numbers than HP numbers and they wanted it over the 400 ft/lb mark. They also needed the torque to surpass that of the 5.0 to try to lure away V8 traditionalists.