Duplicati Commandline options limited vs. Duplicati GUI options?

Depends!

The default installation method will configure the Duplicati engine to start when the user logs on and it stops if they log off. For regular systems this is usually fine, since if they aren’t logged in they aren’t modifying any files.

But in some situations you’ll want the backup engine to run all the time, regardless of whether someone is logged in or not. To accomplish this you’ll want to run Duplicati as a service: