What is the use of PWM over brushless control
You're missing the giant, angry orangutan in the room:
Cost

The OP in the question you are referring to is trying to control a computer fan.
These are very, very, mass-produced devices. There are specialty ASICs available explicitly for the purpose of controlling them, which integrate the hall-effect sensor, the controller, and the coil power driver into one single (generally 4-6 lead) package.



Second, the "brushless motor" in most fans is not a traditional three-phase motor. In fact, most DC muffin fans are one-phase only! The "controller" simply turns power to the winding on and off at certain points in the fan's rotation, relying entirely on momentum to carry the rotor when the winding is not energized.

Given this controller topology, there isn't much you could do to to slow such a system down, except A: Reduce the coil voltage, or B: PWM the coil. Given that the controller is completely stateless (it's just a hall-effect sensor and a power transistor, really), PWMing before or after the controller is basically just a matter of opinion.