Persisting config.inc.php values between upgrades

I have custom values for $conf['interface_logout_url'] and $conf['interface_modules_enabled'] defined in config.inc.php. The upgrade script does not appear to remember these values between upgrades. At the same time, it makes no sense to commit this file to version control as it also contains a version number definition, and database credentials.
If I am reading the code correctly, there is currently no way to remember these values between upgrades. Am I overlooking something? Or if that is just the limitation for now, would it be feasible to add persistence ( @till )? E.g. by making the upgrade script remember them like it remembers the db credentials. Or by adding an 'if custom file exists, include that' to the end of config.inc.php so people can force override with their custom settings?

 

Thanks for your quick response. Pull request opened: https://git.ispconfig.org/ispconfig/ispconfig3/merge_requests/742