According to the COM-HPC module schematics, the FAN_0 header should be controlled by the MMC - I presume according to the SoC temperature. However, I just tested it and despite getting up to over 80C the fan never started running. I've connected the module's fan to FAN_1 for now.
Under Linux, 'sensors apm_xgene-isa-0000' displayed:
SoC Temperature: +87.0°C
CPU power: 45.44 W
IO power: 19.28 W