The default.conf.php file is no longer read by default. There's a large header telling you that it's not read and you shouldn't modify it, but users frequently miss this and attempt to modify it.
This is only safe to remove after we verify that all the settings in default.conf.php are identical to the global defaults. If there are differences, removing it might silently change configuration for installs.
We also need to make sure phabricator_read_config_file('default') continues to work, but can special-case that to just return array() if the file is not present.