You are objecting to a NORMAL design practice!
If you have a fan running and send it signals to slow down it will. But if you keep sending it even slower signals, eventually it will STALL because its electrical feed cannot overcome friction in the fan motor bearings. If the signals are not changed, that motor will remain stalled with a small current flowing through its windings and heating them up, but for no useful purpose. ONE of the things any normal fan header on a mobo will do is monitor the fan SPEED signal sent back to it from the motor. IF that signal indicates NO speed (or, in a few mobos, speed below a set minimum limit) the header will send to the motor a set of signals for FULL SPEED to re-start it. If that works, the header will then return to sending the slow-speed signal it needs for the temperature its sensor reports. In most cases this works to solve the problem. Sometimes, though, the original stall happens because the configuration of the mobo header is set to send to that motor a minimum speed signal that is too low and WILL cause the fan to stall again, so the whole process will repeat.
At START-UP the header does another trick to PREVENT a failure to start. IF the signals sent to the fan were for a very slow speed from the beginning, it is likely that the speed signals would be so slow that the fan would never start. It would be a stalled fan requiring further action. So the normal process is that ALL fans start up at FULL speed on every boot-up. After a few seconds as the POST process completes, each fan header then goes to a normal mode of sending out a speed control signal for the cooling requirements reported by its temperature sensor.
Changing where your fans are plugged in will NOT avoid this full-speed start process. What annoys you is the guarantee that all your fans WILL start up and do their job. If you were to rig some way to avoid that, you might NOT get fans cooling your system.