I wonder what you mean when you say that you "that is why we only installed the cooler as shown above." I thought in your article about i7 cooling tricks, you noted that aligning the heat pipes so that they go across the die results in more efficient cooling. That is why you SHOULD install it that why, regardless of whether it fits the other way or not, am I right?

Well... not to be rude but if it doesn't fit, how do you expect them to fit it in? They try to keep the testbed unchanged. If they change the case, motherboard, etc., just to accommodate proper orientation they will skew the results. These are just limitations of the testbed that were not foreseen initially and this is the price they have to pay. i.e. I can install my Mugen 2 in only one of the four possible ways in my TF8200+. It just doesn't fit otherwise. First, the AMD socket does not allow me to rotate the heatsink and then there is room to install the fan only on one side of the heatsink (barely; fan's still pushing on the SATA cables).
However, I do agree with you; they could have tried to accommodate 25mm (thickness) fans, or at least one if the would have fit. After all why didn't you guys use the same fans as in the shootout?

Jonko