From @Krinkle in https://phabricator.wikimedia.org/T232140#5970936:
@Jdlrobson There are still two unresolved issues:
- The default in Setup.php fills in the old deprecated setting, whereas it should (instead, or also) be filing in the new one. Otherwise, the branch in SkinModule for wgLogo can never be deprecated.
- The installer generates LocalSettings.php files with assignments for the deprecated setting. (work in progress at https://gerrit.wikimedia.org/r/575293)