I see your point, but the controller has it's own 120mm fan blowing directly onto the controller heatsink.I think the fans on the top are the reason that you controller overheats as the airflow goes from front to the top instead the back.
Also the backside is pretty close to the wall (at least it looks like that in the photo) not allowing the hot air to escape.
As someone else pointed out I really need to re-apply some TIM to the processor ad to be honest, I should have thought about that before. It makes sense.
Don't ask why, but I have three of these controllers and I checked one of the spare ones and there appears to be no TIM on the processor at all. It's bare.
But you're right, there is no "natural" air flow around the PCIe slots unless I crank those front fans up to a ludicrous level.