2016 F-53 New 6 Speed trans BUT Less HP, Is It Worth It ?

Personally it would not concern me. Since Ford did not appear to change the physical characteristics of the engine (valve configuration or size, injectors, compression ratio and such) I would suspect the derating is electronic and can be regained with a tuner if desired. Probably tweaked the injector pulse timing to give a slightly smaller charge of fuel per compression cycle. Easiest and lowest cost way to meet requirements. Retooling a production line is something altogether different. Very expensive.