I used the pad when I assembled, rather than doing grease on the assumption that grease the thickness of the pad (filling the gap) might not conduct heat as well as the pad. It seemed as if the pad left no gaps, but I don’t know how much it might have compressed (which is good) since I haven’t disassembled since I assembled it.
The stock software is running the fan against the CPU temperature. I have updated software to get more information on the oled (ala @RayMondDrakon) have the ability to pick up the disk temperatures to also use to control the fan, since it is evacuating the disk vault more than it is needed to cool the CPU.
I have posted that software at: Penta SATA HAT enhanced display (oled, I/O, temp) and operation (button, fan) (though I have updated a bit after that). It has been solidly plugging along for me.
I have both a Quad and a Penta, and actually prefer the Penta since it does not need an explicit fan, and has the always-on controllers, so stopping and starting the service does not drop the controllers.
My Penta, running 4 2-TB seagates in raid-5) is the working storage, the Quad is a play system sharing single disks.