Well, I kinda sorta figured out how to control the fan. One plugs in the fan control wire (blue) in the - pin (toward the HDMI port) of the 2-pin JST header. There is a GP7101 PWM controller sitting on I²C bus 1 at address 0x58, and from reading the datasheet available I'd managed to figure out that you can put in a particular 8-bit value that controls the PWM signal.
i2cset -y 0x58 3 0x00
turns the fan on permanently
i2cset -y 0x58 3 0xff
turns the fan off permanently.
Values between 0x00 and 0xff should cycle the fan on and off at longer and longer intervals. It doesn't seem to be that noticeable below 0xc4 or so as the on cycle is too long. 0xd0 turns the fan on for 1 second with two seconds off. 0xe0 turns the fan on for about half a second with 4 seconds off. 0xf0 turns the fan on for less than half a second with six seconds off. I suppose I should be able to hack the Active Thermal Service package to make use of this method of controlling the PWM fan.
i2cset -y 0x58 3 0x00
turns the fan on permanently
i2cset -y 0x58 3 0xff
turns the fan off permanently.
Values between 0x00 and 0xff should cycle the fan on and off at longer and longer intervals. It doesn't seem to be that noticeable below 0xc4 or so as the on cycle is too long. 0xd0 turns the fan on for 1 second with two seconds off. 0xe0 turns the fan on for about half a second with 4 seconds off. 0xf0 turns the fan on for less than half a second with six seconds off. I suppose I should be able to hack the Active Thermal Service package to make use of this method of controlling the PWM fan.