This is more a status setting. When you are a Channel Commander you can talk exclusively (Whisper) to other Channel Commanders wether they are in your channel or in other channels. When granted the green light in front of your name will change into a permanent red one.
This function comes in handy when you have massive amounts of persons on your server and you want to communicate with leaders only. You can keybind this function in several ways in the Setings - Key Settings menu.