The create folders command is context aware. So if you run it from the project overview page you will only get the top level folder structure without assets or shots. If you run it from a task you will get the top level project structure, the asset/shot folder and pipeline step folder structure for that selected task (assuming you are using the basic tk-config-default2). Same goes for the tank command. If you pass it a Task/Asset/Shot as arguments it will create the folders for it. Without arguments it will just create the default project structure.