I have been wondering about body positioning on the trainer lately. I use a somewhat vintage road bike with a very stretched out position on the trainer and I set my mtb up more trail oriented than XC so there is a drastic difference. I feel like I have without a doubt improved this way but I wonder if those long slow MTB climbs are still kicking my butt because of the muscles being used differently or if its just because I’m at 2.5w/kg.
As far as flats v.s. clipless on the trainer I use clips so that I can complete the efficiency drills. I use a somewhat extreme flat pedal on my FS MTB; the Pedaling Innovations Catalyst Pedal. I and a standard flat on my HT. I can still say that the efficiency drills have helped even on flats.