Thanks for the quick help.
I have configured the cooling zone as a thermostatic fan for now. It seems to stabilize right above the T parameters and that's at least good enough right now. I'll do some tweaking with the pwm range to have it settle betwenn the T values of M106.
The biggest issue before was unstable temperature, so at least that's fixed.
The PWM inversion with M307 didn't work for me. I've also tried to invert the pins unsuccessfully. I think for that feature I'll wait for the FW update.