As far as I am aware the autotiling implemented for the 2d tilemap is not available for the 3d gripmap, so you would need to program the logic yourself too .
You will probably want to write a custom editor in GDScript rather than modifying Godot Engine directly. What I mean is that you would program/run your custom editor as you would program/run a game.
GDQuest's Node Essentials is showing how to use the 3d gripmap node and how to implement a basic autotilling and level editor, but it is a paid resource.
I have made randomly generated 3d tilemaps a while ago with BabylonJS, and I found this resource very useful: http://www.cr31.co.uk/stagecast/wang/blob.html
This video also looks promising:
Hope that helps :smile: