Your questions indicates that you want to control fan speed solely for the benefit of the FAN. BUT ALL fan control systems are designed to ensure that the HEAT SOURCES in your system get cooled sufficiently. They do this by manipulating the fan speeds to whatever is necessary to keep the TEMPERATURES of those hot components under control. The fact is, these systems all are TEMPERATURE control systems that aim to control a TEMPERATURE at a sensor, and do their work by manipulating fan speed.
Normally, there is one system that uses a temperature sensor inside the CPU chip and controls the speed of that chip's cooler. A second similar system guided instead by a sensor on the mobo controls the speed of case ventilation fans. A few mobos also include added sensors on specific mobo components for unusual layouts that have particular fans aimed at those components.
In all cases, although the mobo receives and displays for you the speed of the fan attached to each mobo header, it does NOT use that speed to control speed! It simply sends to each fan a signal (voltage or PWM, depends on which fan type is in use) for what approximate speed it wants, but does not really care what that is. What is DOES care about is whether the measured temperature is correct, and it raises or reduces the fan speed signal it sends out according to that temperature.
An important secondary function of each mobo fan header is FAILURE detection, and this IS based on the speed signal sent back from the fan to the header. If the speed signal falls to zero (or, in some cases, below some set minimum), the mobo sends you a warning message immediately. In the case of the CPU particularly, when failure is detected some mobos even will take drastic action (such as a complete shut-down) to prevent CPU overheating without even waiting for the CPU's internal sensor to show high temps.
It is not obvious, but many of your concerns are already included in the automatic control systems. At boot time all fans are given a signal to start at 100% speed to be sure they start. A short time later as temperature readings become available the speed is turned down to what is needed, then adjusted continuously as temperatures change. All systems are set never to tell a fan to run so slow it might be in danger of stalling. For Voltage Control Mode systems this often is no less than 5 VDC supply; for PWM Mode a similar minimum "% On" signal is kept. Further, in case that process is still insufficient, IF fan failure is detected, the first action usually is to increase the fan speed signal significantly and watch whether the fan re-starts. If it does, normal control is resumed. If it does not, real fan failure is alarmed as above.
Many systems give you an option to specify your own version of a fan speed "curve". That is, what speed signal to send out for what temperature as measured. Using that tool you certainly can set a lower minimum speed than what the mobo makers planned. BUT you need to be aware of two factors on making such a setting. One is: what is the minimum signal your fan can be running reliably without stalling? And secondly, what is the minimum amount of cooling your system needs to keep those temperatures under proper control? Remember always, running fans slower and quieter means you are depriving the heat generators of cooling air flow.