To me this sounds more like "re-position" rather than "move". Therefore Flying wouldn't apply here.
This happens outside of the movement phase, and since flying is only listed during the movement phase the rules do not apply in the shooting phase, or any other phase, except in instances like "There is always a breeze..." where it does specifically state that the move is treated as if it were happening in the movement phase and would therefore take flying into account.
As far as picking a point on a ship or scenery piece...That is difficult because measuring distance is not base to base. So the closest point base to base will always be at the same plane as the tabletop. For pieces without a base you measure base to closest point, but to go in a straight line AND get 3" above a model means you'd have to have so very vertical scenery that has a much broader top than base.
BUT also consider that you have to move in "a straight line" (singular line). Moving to a point high up on the battlefield and then down to the table to put your model takes two straight lines.