I find it interesting that people haven't found their way over to my modifying the IHS of Nvidia GPU's guide yet. I've got alot of evidence of the increase in performance and decrease in temperatures when removing the IHS. Naturally, having two layers of TIM and an added element that needs contact for heat suppression, the temperatures will be higher. Coming from the knowledge I have of decreased temperatures with removing the IHS on a chip, you should experience lower temperatures without the IHS.
Intel may have done a good job with the amount of TIM and the surface quality of the IHS between the area of contact between the die and IHS. However, you won't beat a lapped heatsink directly on the die of a chip. A lapped cooler directly on the die will barely need any TIM at all. The surface quality of the die is glass, its silicon, its the best flat/non-porous surface you'll probably get. The IHS coating of zink I believe, will contain a bubbly texture on the surface, if you don't believe me, hit it a few times with 2000grit sand paper and you'll notice it on the 1st or 2nd stroke on the sand paper. The electroplating of the zink on the copper creates a sort of bubbly texture, that's just how it is. That's why the IHS for all of intel's chips aren't like a chrome like mirror finish. If it was a perfectly smooth surface, it'd be like chrome, or a mirror. That matte finish is the bubbles that you see in the surface.
The article is good for explaining different thermal pastes but I think it'll just be time before we start getting more evidence that removing the IHS completely does infact decrease temperatures quite substantially. I got a good 10C+ temperature drop when I removed the IHS on my 560...
I agree with the 3d transistors causing more heat though! Moving from 1 surface causing heat to 3 would prove to increase temperatures. However, I think it would have higher load temperatures, but in the same, when its idle, you should have lower idle temperatures since the cooling would efficiently reach the 3 surfaces of the transistors to cool them better when not under load....but I dunno...its just a guess