I remember viewing a Unity tutorial on setting up MVC with gameobjects; he described having an empty gameobject for the model, the view, and the controller, and would then place more child gameobjects into those root gameobjects depending on what he wanted each one to do. It was then just a matter of dependency injection. There was no special coding involved, the MVC pattern was implemented in the editor itself.
In Godot, you could think of the base node as an empty gameobject, and then just add more child scenes to the three root nodes (with some 'master' node to hold them.) You would resolve dependencies via get_node(). Everything else is business as usual I would imagine.
