You can use regular navmesh in a WP level. I think if you have dynamic modifiers only, it will include more things in the octree. For example, we use a regular dynamic navmesh in FNBR even though the map is using WP. Lego FN also uses regular navmesh and WP levels, but it utilizes navigation invokers.
3D navigation does not have an ETA. It is on our radar and something we want to tackle. I will push for its prioritization as multiple licensees have requested it.
In virtual query filters, you can override getVirtualCost to add more logic into scoring individual polys while pathfinding. It would not require any areas to be set up. You may need to track more data (which is possible in query filters to host other configurable variables) to check the direction from the previous poly to ensure it is within the tolerance of your turning radius. There are other threads on here with some setup for that. The main concern is perf as it runs on every poly of any pathfind using the filter. For example, we have used similar filters for setting things up with leashes in FNBR to keep them within a certain distance from their anchor point.
Pruning by using seeds offline has been discussed. I certainly see the use of the tool for removing unreached polys automatically.
Thank you for the additional info. It does help us as we discuss and prioritize features for the future.