In the end I use Areas and move one per object I want to collide. Then I set up signals for areaenter( Object area ) and implement my own function for it. That way I can get basic collision in 3d. If you get the GodotDemos zip and unpack it and search through it for examples of 2d Area and onbody_enter() you can start to see how things are wired up and coded up. That's what I did to "learn" how to do it. "Just" use the 3d verison of Area and CollisionShape.
It requires that I use a tree like this for each:
1) Area as parent
2a) Mesh as child of Area
2b) CollisionShape as child of Area, sibling of Mesh.
So the CollisionShape is a hack that is a fake bounding box approximation to my real 3d mesh geometry. Better than nothing. :-) :-(