As I said previously, virtually ALL mobos have at least one temperature sensor built into the mobo at some point the designers have decided is either typical of the whole mobo, or a critical component whose temperature needs first priority. In addition, the CPU maker has installed at least one sensor inside the CPU chip. On every mobo I've looked at recently, the internal CPU sensor is the ONLY one used for the CPU_FAN header. On some mobos you have the option to use that same sensor for other fa headers. Then for all the CHA_FAN or SYS_FAN headers you always have the option of using the mobo temp sensor to guide them. In many cases (such as yours) you have NO other option, so I'm pretty sure in your case it is the mobo sensor used for the SYS_FAN headers.
rascalov has things mixed up a bit. For both CPU_FAN and SYS-FAN headers the normal automatic fan control strategy is to establish a target temperature for the relevant sensor and a few control loop tuning parameters (pre-programmed settings) and constantly monitor the actual temperature st that sensor. If that measurement deviates from the target, the BIOS control software changes the speed of the fan its is controlling. It makes further changes if that is insufficient or if the measured value changes. VERY often you have three other choices. One is that you can set your own target and acceptable temperature range (a "custom fan curve") that works in exactly the same manner but with different control parameters. The other two are usually fixed speeds with NO speed control changes - either full speed or some reduced speed.
Virtually all fans generate within the motor a speed signal consisting of two brief 5 VDC pulses per revolution and send that out on Pin #3 of the fan cabling. The mobo counts those to display fan speed and as a secondary function, checks to be sure that there IS a speed signal coming on - no speed signal (or, on some cases, a speed below some limit) it treated as a fan FAILURE and are warnings sent out. But in fact the speed is NOT used to control the fan speed! The target of the automatic control system is the measured TEMPERATURE, not the fan speed. BOTH 3-pin and 4-pin fans DO send exactly the same type of speed signal on the same pin back the the mobo header.
The older type of fan called 3-pin or Voltage Controlled Fan has its speed controlled when the mobo varies the voltage supplied to it (on Pin #2 - #1 Ground) from 12 VDC for full speed down to about 5 VDC. Any lower voltage may cause the fan to stall. The newer PWM fan design (4-pin fan) requires a different method to control its speed. In this system, the Voltage supplied on Pin #2 is always 12 VDC, and there is a new PWM signal on Pin #4. Inside the motor case there is a small chip that uses the PWM signal to modify the flow of current from the +12 VDC supply though the windings, thus providing speed reduction to whatever is needed. The design of the two systems means that if you mis-match systems and plug a 3-pin fan into a 4-pin header that actually is using PWM Mode as its method of speed control, that 3-pin fan receives the constant +12 VDC from Pin #2 and no PWM signal because it has no connection to Pin #4, and has no chip to use it, anyway. So that fan will always run full speed - you get lots of cooling, but no ability to reduce fan speed. IF you mis-match the other way - connect a 4-pin fan to a header using the older Voltage Control Mode (aka DC Mode), the fan will receive no PWM signal because the mobo does not send one out on Pin #4,but it will receive on Pin #2 a VARYING voltage that DOES control the speed of the fan.
Most mobos now use only 4-pin headers for fans, but that does NOT mean they are using the new PWM Mode always. IF a mobo is designed for it, the Mode (method of speed control ) may be chosen - either Voltage Control Mode or PWM Mode - and very often is set to default to PWM. So such a header CAN control the speed of EITHER type of fan if its configuration is set properly. However, some header do not offer this flexibility and use only one of those Modes. But in any case, BOTH types of headers CAN read and display the speed of the fan IF the fan actually has the wire to carry the speed signal to header Pin #3.
So, all the statements you see claiming the you cannot control or "see" the speed of a 3-pin fan no matter what are wrong. You can not control that fan's speed IF the mobo header cannot use the older Voltage Control Mode, but you can if that choice of Mode is available in the header's configuration. And both types of header Mode can control the speed of 4-pin fans, even if technically the Voltage Control Mode is not as good as the new PWM Mode for 4-pin fans.