I'm not a fan of recessed pedal either... my reasoning is the recessed pedal causes your center of balance to be more "forward" while on the TM. Being that I fish shallow stumpy lakes most of the time, when I hit something and it brings the boat to a complete stop I'd prefer my balance to be back of center to keep me in the boat and not doing a swan dive over the trolling motor.
Yeah the thought of it seems kinda awkward to me. It definitely seems like it would have you off balance. Best thing I ever did for my back is adding a stool type seat up front. Went seatless for years because I never liked sitting down while fishing and thought the stool would be the same, but I got one and I love that thing.