One, I think you're making a statement that just isn't true without qualifying which engine's you're talking about. I own an automatic 6.0 (2006) and a manual 6.0 (2005). They both have the same sticker on the valve cover, 365hp. No power pulled when they installed the third pedal. My 7.3 manual was same as my 7.3 auto. I guess I'm not sure about the 6.4L Ford, but I didn't ever remember reading about a 340lb/ft derate, and the 6.7L never had a manual behind it, so I'm not sure what motor you could be talking about.
Two, you're giving up more power to the wheel with an automatic as there is an inherent loss when you're fluid coupling the motor to the drive axle, so even if they hold back a few (as they do in the case of the Dodges), you're also gaining a few to the ground. When I come off the clutch on my truck, it's mechanically coupled (obviously there are parasitic losses, minute slippage, etc, but nothing like an unlocked torque converter).
Three, it's all in the tuning...so when I put a tuner on my truck, the factory tuning would become null and void anyway.
My $0.02.
That said, I think after rereading, maybe you're saying you lose 340lb/ft comparing the new manual Dodge to the new automatic Ford? In which case...point's 2 and 3 still apply.