Funny, I think you have a misunderstanding of basic engine dynamics, and / or how a supertrapp pipe works.
First, the cooler the air the better fuel burn you will have so your theory on the temp difference is just a little back assward, ( higher intake temps equal less power not more )
Second, the principle behind the Supertrapp pipe is that the amount of back pressure is completly adjustable, This is done by adding or removing the plates you see stacked on the end of the pipe, this will either increase or reduce your back pressure depending on what actions you take.
Third, back pressure is primarily required to retain torque, because you can add a free flowing pipe to your bike and gain peak horsepower numbers and loose a significate amount of torque.
Fourth, props to rob for using this set up, you can achive great results using these pipes but it adds a whole nother dimension to the tuning process. Tuning the exhaust while tuning the FI can take weeks.