Hi, I don't think motherboards have a minimum PWM % they can send the fan, more like a minimum programmed in to the BIOS/UEFI.
My experience is over-ridding with Speedfan (or the like) allows you to send what ever PWM % you like to the fan.
How it reacts to that is another matter.
You might take a look at the official spec document,
pages 12 -16 are the interesting ones.
All the PWM fans I've used have bottomed at at 25-30%, sending a lower PWM has made no difference to minimum speed. I have TY-140s on my CPU cooler and also find the minimum speed to be ~690rpm @ 30% PWM. According to the official doc it should be 30% of max speed, ie 30% of 1300rpm = 390rpm (+10% allowance = 40% = 520rpm) which I would much prefer to 690rpm minimum.
However... I've wired a Zalman fanmate in to the +ve and -ve wires of the fans so I can adjust the power supply voltage the fan sees, the speed and PWM wires are still directly connected to the mobo header. What this allows is to adjust the operating range of the fan, with bit fiddling getting the right level I now have a 500 to 1000rpm fan. (still on PWM speed control and reporting its speed)
Some Scythe PWM fans come with a back plate fan controller that has two modes. (IIUC) In one mode it directly controls the fans speed like a normal 3pin fan and controller. In the other mode it acts like my fanmate, the fan's speed still varies with PWM signal but the range it opperates over is adjusted. E.g. you can set fan to be 500 ~ 1600rpm range or 300 ~ 1200rpm or whatever you like in between. Scythe fan with controller
Hope this helps, Seb