Currently, the latest documentation on command line options is in the help file.

The /noninteractive and /noprefs command line options existed before version 2.14 but were not documented.

/noninteractive: it prevents the display of any message boxes and exits WinMerge as soon as the comparison is complete.

/noprefs: do not load settings from the registry when the option specified.

You can export settings by clicking the Export button in the Options dialog.