I realized I'm able to use the scope attribute (the most important to me) inside WP_Query. But they only accept 'past', 'future', 'all', 'next-month', etc... They don't accept '2012-02-01,2012-02-28'. Do you know why is that?
About the custom taxonomy querying, I think that even creating a hook for the join issue is not a great solution. It will probably work, but would still be very hard for regular users to integrate custom taxonomy to their events.
Maybe a custom hook that register the taxonomy, by the name, for the Events Manager plugin, fully integrated?