The screenshot that You linked shows that in case of the CHA_FAN1/2 connectors the 4th pin i.e. the PWM control line is connected (directly) to +5V. Therefore, these connectors really are 3 pin connectors, or fake 4 pins if You'd like.
As Andrew said, real PWM control needs four pins:
- power (+12V)
- sense line
- control line
3 is where the fan can report its actual speed to the motherboard.
4 is where the motherboard can send the pulse signal to the fan.
The pulse signal tells the fan how much time it should run at full power. So, for example, if You want a PWM fan to spin at half its full speed then the following happens: the fan motor runs at full power for a while (half of the time), then it coasts for a while (the other half of the time), then at full power again, etc, etc i.e. it gets pushed by +12V periodically. The portion of time in which it runs at full power is called duty cycle. The important thing is that the switching between full power and coasting happens really fast - the frequency of the pulse signal is tipically in the few kHz range.
In conclusion, the 4th pin tells the fan what portion of time it should run at full power and the 2nd pin provides the power for the "pushes".
In our case, the motherboard is using a trick to control the PWM fans that are connected to the CHA_FAN1/2 connectors. It doesn't modulate the pulse signal to lower the speed, it fills the signal with +5V and variates the power voltage instead.
The only problem with this is that some PWM fans produce a weird buzzing noise if they get lower than +12V as power.