They are not directly comparable unless you are going downhill. 200 watts is 200 watts. If you're going DH on an mtb, I agree that the beating you take in your joints, upper body, and back does contribute to your fatigue.
Try to ride a steady 18 mph over a rutted road, and tell me you don't take a beating.
Some roots really killed me two weeks ago, on a ride south of Toulouse. And even though on an MTB you wouldn't even notice the irregularities very much, on a road bike these slight irregularities become a pace eating torture.
Those irregularities (and a vicious set of climbs from roughly the 60 mile mark) absolutely did it for me, and contributed to a lowly ~16.5 mph average over 70 miles.
Also, MTBs have these super tiny ratios. When I hit a 9% incline, my cardio and setup don't allow me to stomp up the hill at 90 rpm, and my legs (and torso/back) have to take the extra force required by the lower rpm and "round pedaling". And I refuse to mount a triple

On an MTB, there's always a smaller gear.
But I'm looking at MTBs, mostly as an off-season toy, when I don't want to get my road bike dirty.