I fly both 3-axis microlights, and SEP aircraft, often jumping straight from one to the other, and have to agree that it does take a bit of thought.
The landing characteristics are very different, you come in incredibly slow, and have to roundout/flare at a comparatively low height.
Also, the controls are generally reversed, from yoke in right hand, throttle in left to the complete opposite.
Very good fun though, awesome take off and climb performance, and at 12 litres an hour much less costly.
No problem at all with confusing the controls of a weightshift to 3-axis, the sensations just aren't the same.