When you start Fabric (using the Application.run() method), Fabric will fire the GTK main loop and start a DBus client, which allows you to execute code on-the-fly and get information about your configuration file. Fabric grabs your global and local environment so when you run code via the DBus interface you get access to all of your variables, objects, and/or modules.
The CLI utility is just a command line tool to use the DBus interface instead of dealing with DBus communications yourself.