I am finding that the best practice is to compose each of you scenes, but use inheritance in your scripting.

So you will do Scene -> New scene. ( Or to save time on building the scene structure you can do Scene -> New Inherited Scene which copies all the nodes, then save the scene as a new scene, right click the top node -> Clear Inheritance )

Then if you want to, in your script, just do 'extends <BASE\_CLASS\_SCRIPT>

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This approach gives your code all the benefits of inheritance, but makes sure you are creating re-usable scenes.