... for sub-folder multi-site installs.
I don't see why you can't do it by hooking in to the do_robots.txt action.
The old Sitemap plugin I use to use did it just fine (search for robots) -> http://plugins.svn.wordpress.org/xml-sitemap-feed/tags/3.9.2/XMLSitemapFeed.class.php
I managed to write my own filter to handle this but just thought you should know that it's not that hard to do.
Great plugin by the way. I really appreciate all of the hard work you clearly put in to this. So happy to see sitemap index support. The old plugin would constantly choke on too many URLs.