Not sure you are getting it...let me try again.
*3-pin or 4-pin headers on motherboards can use CPU temperatures to control their speed (typically on the CPU header). This is not true on ALL boards, but many have that ability to use CPU temp on the CPU header to be controlled either by 3 pin (voltage) or 4 pin (PWM).
Some may only be PWM or only voltage, others both (Today we are seeing a lot of both on the boards ). It simply depends on the the board and BIOS as to how a fan header can control fan speeds (voltage/pwm). Typically the CPU sensor works off of CPU temps. Again, it will vary wildly by board. In fact, my ASUS board has the ability to control fan speed with 3 or 4 pin AND the ability to select which sensor to monitor to 'control' it (includes CPU, board, VRM, etc) on each headers. This setup is not common however.