Depending on how your scene is setup, you might be able to generate a Navmesh using the SurfaceTool. You can find an example of this type of Navmesh generation on a PR I made to the Godot demo repository. (I need to update the pull request soon...)
As mentioned in this post here on the forums, CSG nodes/meshes would be ideal an candidate for this, but right now it doesn't appear they are usable for Navmesh generation.
Hopefully this helps! :smile:
