In Branch Explorer, it's hard to combine inclusion and exclusion rules since there is no way to adjust priority order between them, and exclusion always seems to override inclusion.

I would suggest evaluating (for each branch) the inc/exc rules from top to bottom and stopping at the first (enabled) matching rule (just as for the custom coloring rules). Then you could re-use the "move up" button for adjusting these prios (only keeping the separation of color-rules from the inc/exc rules).