Are you sure about that? The cases were designed to be stackable. Also air is not likely to pass through unless you are actively pushing air against the underside of the case.
I agree though that aluminium is the ideal metal to use.
I'm only speculatively certain about the spacing and have no contact with the person who did design it and no experience in case design. Though, it makes sense.
If you put heat paste between the heat sink and the base heat will dissipate into the structure better. If the ambient temperature of the outside of the case is cooler than the inside the case then the case, due to it being of aluminum, should be acting like a heat sink due to extra surface area from the case being added to the heat sinks. If you were to stack the cases without the spacing heat would pass from one case to the other and wouldn't exactly dissipate as well. There's small spacing between cases as far as I can tell from pictures of people stacking them.