are you sure it's running cooler? or is it that it feels cooler to you? those two are not necessarily the same. a few years back, I was doing the same thing, so I did a bunch of searching. not sure where I found it, but found a good study where a guy had done some very specific measuring with highly specialized and accurate equipment and found that with the doors closed, more air was forced over the cooling fins and the engine temps were lower. on the flip side, because of the doors being closed, and more heat being pulled off the engine, it felt hotter to the rider. but if he opened the vent doors, his perception of heat went down, but less air was being funneled directly to the engine and engine temps were higher.
he did this several times, and was able to get repeatable results. now, granted, the engine temps were not drastically higher or lower, it was in the neighborhood of 1-2*, so really not anything to get worked up over.