Set Default Date format in PHP

Yes,there is a filter here: https://github.com/stephenharris/Event-Organiser/blob/develop/event-organiser.php#L172 which allows you to modify the setting values.

But that won’t help you distinguish between a ‘default value’ and one set explicitly by the user.

You could instead use a hook provided by add_option (the plugins settings are stored inside an array with option name eventorganiser_options) to change the default settings when they are initially added to the database.