When you start fabric (using the start function), Fabric will start executing the GTK main thread 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 execute code using the client you get all of your variables, objects, and/or modules.
The CLI utility is just a command line tool to use the client instead of dealing with DBus communications yourself.