Your concern about muscle memory is unfounded. All pedals, regardless of intended use, move in circles. Unless you have 165mm cranks on one bike and 190mm cranks on the other, there will not be a noticeable difference in pedaling and the pedals you choose have no impact on this. As for unclipping, virtually all pedals unclip in the same manner. I have been using SPD pedals almost exclusively for the past two years and over the past week I have began riding my bike with look-style pedals and the only problem I have found is sometimes I struggle for ~2 seconds to get the pedal flipped into position because I never had to flip the SPDs.

However, there is no reason why you should not use road pedals on a mountain bike if you are riding trails or gravel roads that seldom require dismounting or walking.