I have configured my uninstalled applications in a config file but it is not using these as it say "Configuration Locked".
Initially it did work before I uninstalled anything form the UI, but once I uninstalled an application and then installed it again, it didn't use my configuration file settings.
I noticed that before I set anything, phabricator.uninstalled-applications was set to `null` in the database but once I reinstalled everything it was set to `{}` instead.