There's some hard low-limit for the CPU-FAN connector. Plugging the chassis fan into it (a standard 8cm fan) it runs quite fast (and noisily) even setting pwm to 0.
Conversely, plugging the cpu fan into the CHASSIS-FAN connector I can go below 1000rpm: 700rpm with pwm at 80/255. Lowering further the pwm the fan stops.
It's just how those fans work: roughly simplifying, in a PWM design the fan is switched on and off accordingly to the duty cycle of a modulator signal through the fourth wire: a bit more precisely, the average value of voltage supplied to the fan is controlled by turning the switch on and off at a fast pace, so that the longer the switch is on (with reference to the off time), the higher is the average voltage supplied to it, and therefore the faster the fan spins.
So, where that fourth wire does not exist (as in 3-pin fans), the speed isn't (cannot be) varied at all by the PWM header.
On the other hand, when a you connect a PWM fan (4 pin) to a voltage controlled header (3 pin usually, but also some fake-4 pin ones), that header is still able to vary the fan speed, just directly reducing the voltage supplied to the fan (and possibly get rid of the PWM profile "stored" into that PWM fan, if any).
Providing the Linux fancontrol may control that CHA_FAN header, accordingly to the CPU temperature sensor (as lots of Windows utilities do), you can use the CHA_FAN header to gain those further 200rpm of quietness.
With reference to your PSU, you might swap its fan.