That would be true if it was a fact but im sure its not.
The heat coming off the back of the PCB is equally as hot as the air coming off the fins. I had 2 reference coolers before and the top card was still way hotter.
I have my cards totally open so the air can leave the case and the bottom card is 65c at FULL load! and the top card is 85-94c at the same time. So the Air in the case is not the problem its the air being heated by the back of the PCB on the card below. You only have to feel how hot it is to see whats happening.
Im going to get a new case and use the other PCI 2.0 slot to give me space. Or i might upgrade to Haswell Hex core and a new bigger motherboard.
That's because non reference designs generally push a lot of air down to the motherboard, which then comes back up into the fan because it is blocked by the back of the other card, thus a recycle effect takes place where heated air from the top card is constantly recycled over and over through the design itself.
Non reference open air cooling was never designed for stacked MGPU configurations, it performs poorly in the same conditions reference does not.
Pretty easy way to see this is to remove the mobo from your case, take a piece of cardboard about an inch thick and wedge it between the two cards to create a V between the two. Then place a 120mm fan on top of the cards towards the back blowing down at the motherboard.
You should see a 10-15C drop in temps at the same fan speed, the reason your current method of removing the side panel and using a box fan isn't working is because it isn't actually addressing the fundamental problem with non reference designs in MGPU.