Well Yes and No. What you want is cooler and easier air flow. The headers are not close enough to the manifold to heat them up significantly. So your right in a sense, the can get warmer. However because of the bigger piping and the Cone Air filter. The flow rate is much quicker and whole lot more. I actually thought of the same thing as a concern. So to help, what I did was use apply a few heavy coats of insulation paint. It is formulated specifically for automotive parts that will be in a higher level of heat area. So with my system tube heat isn't effecting my tubes. I physically so that, that minor improvement brought down my over all engine temperature about 25%. It's really neat stuff how it works.
So now looking at the Pro's of the system: A lot less restrictive, there is a whole lot more do to the 3" piping, and it is staying cooler because of the insulation factor. Over all, it doesn't get much better... Or does it? No I have some plans for the future, but I'm in the very beginning stages of testing. So you won't see anything for a while. I hope this answers your questions.