Mike Tee,
It pretty much depends upon the machine and the conditions. Bell recommend the application of the rotor brake below 38-39%Nr down to an almost stop and then to release it.
The idea being to stop/prevent excessive blade sail as the rotors slow down. The correct action would then be to install a blade cuff and tie down to prevent the windmilling you describe. A touch of laziness crept in perhaps? Occasionally, if the weather was benign there are some who would roll to ground idle and let the blades windmill without chopping the engine or applying the rotor brake. This has led to a few dynamic instability roll overs that I know of!
On the bigger machines the rotor brake is applied whenever the rotors are stopped and not cuffed. This is especially important on machines with fully articulated heads as the flapping/dragging/feathering hinges allow for quite a bit of movement in windy conditions.
The idea would be to stop the blades clear of the tail boom in order to prevent a tail strike. I have seen the S61 composite blades hit the ground during a squall on deck!