I’m not sure your mental model matches mine, but in my “real job” I deal with the shadow and virtual DOM. Maybe that’s the metaphor you’re looking for?
I’ll have to be a little practical and hope it makes sense. The tree in the editor is the same tree. Godot engine is written in Godot engine, so what is the distinction between being in the editor and being in the game?
The answer is that godot will ignore all project scripts by default while you are in the editor, but it offers mechanisms to enable them. The main way is a keyword in GDScript.
In Godot 3, you put `tool` as the first line of a script, and it will be loaded. Godot 4 has grown a pre-processy decorator syntax, so it’s the same, but `@tool`.
In your scripts, you can detect whether you are in the editor by checking `Engine.editor_hint`. You can do amazing things with this.
Then you can take it a step further, and convert your tool scripts into an addon. With an addon, which is just a directory structure for assets, your custom in-editor functionality becomes indistinguishable from native godot behavior.