You can use https://docs.moodle.org/403/en/Configuration_file#Forcing_the_value_of_admin_settings (be sure to check that your Moodle version includes this feature, as I don't know in what version it was introduced).
In any case, all configuration settings for all plugins are stored in the database, which I assume will be persisted outside the container. Otherwise it will start empty every time you restart the container(s).
Saludos.
Iñaki.