It’s likely that the position of the saddle in relation to the BB is quote different on your MTB, which is why you are feeling muscle strain. Depending on your MTBs seat tube angle and seatpost setback, I’d be adjusting it to get as close as possible to my road bike position. Next thing to sort is the bar position which affects hip angle how open your chest is etc.
Drivetrain drag on a much dirtier mtb drivetrain, see this previous topic 25w delta at 160w! Drive Train Loss - Equipment - TrainerRoad
If you have one of those fans that sit on the floor, put it up on a box/crate/step whatever you have lying around so the air is blowing on you.