Say you wanted to create a subtheme in sites/foo.example.com you still get prompted for enabling the theme / setting the theme to default. This is problematic because that currently happens globally. I believe that we will have to implement checks that validate whether the theme can be enabled after it has been created (by checking if it can be discovered by the current drush scope / drush site alias in use). That's the only reliable way. I guess that's enough really.