If you want the installer to create the active configuration directory (currently complete used) but specify a staging directory - you can't. This situation is likely to be quite common as the staging directory is the one we advise people to keep in git.
This issue will allow a user to add
$config_directories['staging'] = 'staging2';
settings.php before running the installer.
Update the active&stage directory creation code, so that it creates new directory if not set already.
User interface changes