You are perfectly right, but AFAIK this setting only applies to 4 pinned fans. Mine is 3 pin only, hence the "Speed Control" pin4 isn't connected to the fan. So, the "Manual" setting doesn't do anything to any of the 4 fans connected to SYS_FAN1/2/3/4 since none uses pin4. I can even go up to "2.5 PWM value/°C" ... no change in fan speed!
However, when starting up the PC, SYS_FAN1 starts with 380 RPM and gradually reaches 600 RPM after 5 minutes. I have the impression that the voltage on pin2 is linked to the CPU temperature (or any other temperature)?
... later ...
I noticed that setting "1st/2nd/3rd System Fan Speed Control" to "Disabled", I get my 12V !!!
Thanks for the kick!