it's rare because Fan1 is working at 1000rpm and fan3-4 and fanA is working at 2400rpm
They're different fans.
The closed-loop control controls the temperature, not fan speed.
Warning: Control Theory ahead
Fan speed is just a (vector of) state variable(s). System state is multiplied by the output matrix and the result is the temperature you want to control.
The system has quite a few state variables besides fan speeds, even in a simplistic approach: Two or more per fan, relating PWM input and "airflow" output, at least one for the system whose temperature is to be controlled, plus whatever the controller has.
Of course, engineering practice here is to say "Screw this, throw in a PID controller".
Fancy controller design relies on knowledge of a good model of the system, which is not practical in the case of PC fan control. So the default option is to throw in a PID, probably with small k_I and k_D, and then add a bit of adaptive control ("the fan crapped out, set them all to max and try to recover or compensate", though not very fancy, is technically adaptive control).