I have found the flag that enables this filter to apply to route-finding, and I have turned it on (for beta6) - it may not be useful for long-range travel, but is useful for explorers: eg if you want to "go to the other side of this nebula via stars I haven't yet visited" - If it fails to find a route using the filter, the route is left unchanged
Ah great! Thanks! Other people had indicated that you couldn't filter by visited systems. It would filter on the map, but you couldn't actually use it for routes.