The "CLI configuration commands" are stored in /config/config.boot (after you issue the save command when entering tem). So if you want to backup only that all you need is /config/config.boot.
There are additional configuration files, encryption keys, scripts and other files stored anywhere in /config/ path.
The download configuration from GUI will tar the entire /config/ directory (and everything under it) .... this is your FULL backup.
To gain access to the router if you messed up you need console cable like one here.