To be sure, there's a happy medium in there somewhere. I have my MTB seat lower than my roadie so I can get off the back of the saddle if necessary (with the pedals leveled). I'd suggest trying it down slightly.

Of course, the geo of both bikes will play a factor in what you find is comfortable. Some MTBs have much longer top tubes than others which, in turn, affects how much you are leaning over the bike and pressure on the shoulders too.

One thing about the road v. mtb set-up too is that on the MTB, even with my full suspension, I'm out of the saddle more than on my roadie.