At this time, ModeShape can only handle the queries by using the internal Lucene indexes.
We designed the query framework so that we could either handle the queries internally using the Lucene indexes (as you describe), or push the queries down to the connectors so they could handle the queries as necessary. Our priority was to use the internal Lucene indexes (the former), as none of our connectors at the time uses sources that had sufficient capability to handle queries. And we simply never have hooked up the latter approach of pushing the queries down to the connectors. It's really almost there, but we've just not had the time to go back and dot the i's and cross the t's. Part of the problem was that we had no connector to even integrate this with, but now we have the JCR connector.
I don't think we have a JIRA task to cover this, so if you log a feature request to capture it, I can look at and try and get it working. Also, it'd be a great help if you could test it once we have it in the 'master' branch.