An "override option" like e. g. -nogui would come in handy anyway, regardless of what the configuration file specifies
Because it will set you free from following these 4 steps:
- you need to load up the config first using the -f option
- you need to untick the "Show GUI" option
- you need to save back the configuration file
- you start the config again with the -f option, all right this time.