Second that… sitting on top of a hot processor and big pieces of various metals is probably the main challenge of any autopilot HAT. Still, you could always use a ribbon cable of limited length to get more space between the two. Especially with 3D printer access, you could probably mash-up a case with a good gap.
You could even add some sort of ground plane/isolation on top of the mainboard (heat and interference source) to even-out the compass calibration, or go for the extreme and make it a heat sink like my wacky idea for the Pi Zero here: New Raspberry Pi Zero... Will It Work? - #26 by CodeChief 