I can imagine the heat issue will be a minor problem. I fitted under seat exhaust on my 02 R1, but the exhaust system pipes did not run directly under the driver seat, but alot side the bike like an RC51. From my experience of the 02, I found a good amount of extra heat feeding into my legs on the side of the bike.
I can only speculate that with the 04, having the heat travel directly upward to the driver seat, you have to consider the blockage from the plastic to the seat itself.
you might find more heat coming from the sides of the bike to your legs as I experienced on my 02..possibly then flowing towards your ass while riding.
I have no doubt my ass will be one hot cookie during hot summer riding, although I highly doubt it will be as extreme as some journalist are reporting. I think it seems as a big issue because this was never a problem with previous R1's, but it shouldnt be any worse then a Ducati, considering the duc seats themselves are thinner then paper, and doesnt leave much room to push the heat left to right..then travel entirely upwards.