I'm not a tree house builder, but do have some training in structures.
Seems to me you are asking for problems if you have a ridged structure with both the deck and the roof fastened to the tree. As you note, the tree is going to move when the wind blows. The higher up you go, the more movement. So, you risk having the tree trying to move the roof a greater distance than it would try and move the floor.
Might not be enough movement to matter. But, just to be safe, I'd let the tree pass through the roof with a wide enough opening to account for wind movement.
Alternatively, you could fasten the floor and the roof to the tree and leave a gap between the roof and the walls - so the roof would float above the walls.