I know the rules say everything underneath the template is hit, but there is a contradiction in plain view when it says you put the template at the base of the model firing it. Obviously nothing will be under the template when it is lying flat on the ground. In the previous example with a rhino on the hill you have to angle the template. There is nothing in the rulebook that says you are not supposed to aim the template at the target and play in two dimensions. It is a three dimensional game.
As for the 3 foot high flying stand, well that is just ridiculous. It comes with a perfectly viable stand. Alternating it would be bad form, just like targeting two different units...