pwmconfig attempts to stop fans to determine whether it's possible to control fan speed. If fans don't respond to the stopping signal, pwmconfig assumes it's not possible to control the fans. However some motherboards or BIOS configurations seem to protect the fans from stopping, but it's still possible to set non-zero fan speeds. For example after sudo su I was able to echo 20 > /sys/class/hwmon/hwmon2/device/pwm1 which set a very slow fan speed and echo 120 > /sys/class/hwmon/hwmon2/device/pwm1 set a much higher speed - so obviously fan speed is working perfectly at least in this range. However if I try to set a very low value (between 0 and 17) the fan speeds up probably as a result of the mainboard or BIOS protection.
pwmconfig should take into account that sometimes (on some mobos or bioses) fan speed control is only possible in some range of speeds and/or stopping the fans is not always possible even though fan control works
Are you sure it actually speeds up when you set it too low? I have noticed that the Intel stock CPU fans seem to have a minimum speed they will refuse to go below, but when you try, it just refuses to go any lower rather than speeding up.