The acquired data show two clear conclusions. First, that the conventional position for the heatsink, with the fan facing the front of the case, blowing air from the front panel to the rear panel, offers worst cooling performance than the position with the cooler rotated in 90 degrees, with the fan pulling air from the bottom to the top of the case. It is probably due to the fact the hot air has the tendency to go up, and it is easier for the cooler to work according to the natural airflow.
The second conclusion is that there is no advantage in letting the heatpipes to point up. The CPU temperature was actually a little higher when the computer was laid down. The reason for this seems to be also that the case was designed to have an optimized airflow when in its original position.
In summary, at least in our system, the best way to install a tower cooler is with the fan facing down, and the computer case in the vertical position.