I just saw this question How do I eliminate PWM noise when driving a fan? but cannot think of the reason why is doing PWM over brush-less control useful.
I am assuming people are trying to control the torque or speed of the motor by PWM. But ultimately the torque, the speed and the mechanic resistance will reach a balance. So controlling one of these three factors should achieve the original goal. For a brush-less motor, it's much easier to control the speed because the controller is doing that anyway - it determines when to energize a coil based on the current rotor position. If the controller delays energizing the coil, the torque will be reduced.
From the answers to the original question, it seems this (doing PWM over brushless control) is rather common. However to me it's more like a dirty hack when there is no access to the controller.
Am I missing anything?