Oh yeah, it probably is time to start mentioning the version. X)
It is in 2.
The problem lingers in the editor side of things. Generally, haven't had this problem with other things, so it makes me think maybe there is some kind of timing issue with how things are being created and entering the scene. Haven't been able to tease anything out.
The shape in the CollisionShape2D initially would say something like "CapsuleShape2D", then when the scene saves, its name changes to the scene's name, and will not generate any shapes when the game runs. Not until I go through them and click Make Unique. That seems to fix them, yet I'm making this tool to save time since there will be hundreds of these things.
But I think I've lost enough time on it, that I'm just going to write
_draw() code to show the potential shapes in the editor, and then use
add_shape() at runtime.