Some brushless fans use the peak input voltage to determine their speed, some use the average input voltage.
The two typically have very different brushless driving mechanisms, that mechanism determining which (peak or average) ends up defining the speed.
I personally haven't investigated how the two are implemented, only observed the practical differences. (Specifically, that many, but not all, 4-pin 12V PWM fans can be voltage-controlled using three wires, not connecting the PWM input at all, controlling the speed using voltages between 8V - 13V. Some will only run at max speed without PWM input.)
The fan itself has a small PCB on the hub where the wires connect. For most fans (certainly all 3- or 4-wire 12V fans with tachometer output), this includes a Hall effect sensor detecting two pulses per rotation. For all brushless fans, it includes the full or half bridge(s) needed to drive the coils, and the controller for timing that, often integrated to a single tiny chip. It is this IC (and its operational principle) that determines the fan behaviour.
As an abstract example, consider a driver with a constant current input, followed by a low-pass filter. These would be controlled by average input voltage. Now, compare to a buck-boost driver with bulk capacitance on the input. These would be controlled by the peak input voltage.
In practice, the fans use highly specific driver ICs that include things like the initial start-up peak (to ensure the fan starts rotating even at lower input voltages/RPMs); so one can consider them to be controlled by small microcontrollers, and just knowing/assuming that some are controlled by peak voltage, and others by average voltage, is the most useful model.