That's if you want to change it dynamically. But if, for example, the save option has been disabled, the command will not be grayed out. So if you use this method, be sure to use it before the script disabled any command in the command window.
If you want to avoid that, go in the Window_Command class and search for normal_color.
Then change it for Color.new(red,green,blue,alpha), or any predefined colors.