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I am not sure if this is a bug or a "feature". When I create a linked copy and try to disable some objects from rendering, it disables them globally in every scene unless I make new scene a complete duplicate.
See the gif for what I mean..
You need to use the Collection checkbox.
It removes the whole Collection from the current View layer.
You can then use different View Layers, or different Scenes.
Works with linked Scenes or different View Layers
Required, but never shown