Upgrading Moodle via CLI restores the admin settings to the default values, losing the current ones, the way to specify settings values is creating a local/defaults.php file (http://docs.moodle.org/22/en/Administration_via_command_line#Custom_site_defaults) but there is no automatic way to fill this local/defaults.php with the current values. To allow that automatic local/defaults.php settings population without core modifications it could be a new moodle flavours feature.

There should also be a CLI script to access the feature to allow it's execution before admin/cli/upgrade.php

To take into account, files under wwwroot "shouldn't" have write access, so the local/ directory permissions should be checked and return the PHP code to paste in if it's non-writtable. On the other hand there could be a "warning overwritting local/defaults.php"