My idea for a FHS-friendlier setup was based in storing the LocalSettings for all installed wikis inside /etc/mediawiki.d, all of them pulling from a CommonSettings.php where default overrides and extensions affecting all installs would be stored. The update process would just need to iterate on them running update.php
Then for the installer we could ask the user to overwrite a file with the download, overwrite it ourselves from the web installer or create another installer, this one to be run from command line by dpkg.
Does anyone see a problem with that approach?