We might still need a more abstracted view, for logic that is not directly connected to 3D objects.
Could you give a example of a script that doesn't belong to any object?

Well, of course, in Unity, every bit of logic is connected to an object in the hierarchy. But sometimes there's a lot of logic. And sometimes the object is just an empty object (and thus invisible). Logic that is primarily calculations, arrays, loops and conditions. An A.I. system would be an extreme example, or any sort of Finite State Machine.
But as I mentioned, perhaps elements of abstract logic could also be presented in the 3D space as objects that are not rendered in the game but only visible in the scene viewport (or you could simply put them on a layer that the game camera doesn't render). It might be very intuitive actually to manipulate logical "objects" in a similar way as actual 3D objects.
An array could be a stack of cubes with physics properties!