I’m happy to announce that the ability to query multiple taxonomies is in WordPress Core, as of version 3.1.
However, there still is no ability to make use of that feature without writing at least a few lines of code.
So, the focus of this plugin will be shifting from enhancing WP’s taxonomy querying capabilities to providing an awesome user interface for them.
Besides several bugfixes, with version 1.4 you can now choose the order in which the taxonomies appear in the drill-down widget, by simply dragging them up and down.