So maybe use the trainer power instead of power match to a sketchy source?
Yes, SPD-SLs on my road bike and Eggbeaters on my mountain bike. I have had several high-quality bike fits for my road bike, and I eyeballed everything on my mountain bike.
I did another workout this morning, and I decided to listen to my body more intently. A few observations:
- Indeed, my quads are taxed more, I can definitely feel that. After a rather short and easy threshold workout, my quads were tingling while the rest of my leg muscles felt bored.
- I noticed more quad activation on my commute as well. However, my commute is only around 20 minutes long (about 8–9 km), so I don’t think I ever get to a point where they really fatigue. Different story on a trainer, obviously.
- Even when riding smoothly on the trainer or on a straight piece of road, I have noticed significant second-to-second variations in the displayed 3-second-smoothed power on my Wahoo Roam v3. That strikes me as odd as 10+ W changes in 3s-averaged power need even larger differences in instantaneous power.
- Putting the fan on a box really did the trick, cooling is now less of an issue. Although now only my upper body is cooled.
Overall, I am surprised how big of a difference the bike makes. It shouldn’t surprise me if I think about it, but still. I think my next non-bike bike will be a Caveworks Rivet so that I can play with the fit a little. I’ll ask my wife if a Caveworks Rivet counts towards my two-bike limit — can you call it a bike if it doesn’t have any wheels?! 
this seems to be the smoking gun - or part of it. I’d use the trainers power instead. you copied your bike fit from the roadbike to your MTB. Have you considered sag, when setting seatheight and offset from the bb? I’m sure it’s not much but if you’re really sensitive (as I am) then you’ll feel those couple mm difference. I assume the other measurements are the same or comparable? I would assume that seatposition relative to the BB is the most important figure as you’re working with your legs and core rather than arms.
Two things I’d do: check touchpoints of your MTB against your Roadbike once you get it back from the shop. Use your trainres power instead of the pm from the MTB.