The heat in the seat is an issue for sure. We bought a automotive hood liner then cut a piece that will fit under the seat but did not try to use the adhesive to actually attach it to the seat. Went for a 200 mi. ride yesterday and the seat seems much cooler.
The hood liner is about 1/2 inch thick but compresses easily.
Here's the link to the hood liner:
Dynamat.com | The Hoodliner for Automotive and Restoration.
So far, this seems like a fairly inexpensive fix, although until the aftermarket comes up with exhaust system to get rid of the catalytic converter yet still keep the panniers, I don't see a way to really get rid of the excessive heat, particularly when stuck in traffic.