- Edited
It doesn't say a scene is not a class, because it is, the root being SceneTree.
We must distinguish between the representation of data and that of programming logic, and what's inheritance and what is composition. A lower node in a tree of inheritance inherits from the upper levels, but can additionally (or replacing) have other traits. See a script like an object being attached to a node in the SceneTree, but not inheriting from the node itself. Or, more abstract, a representation of the behaviour of an object in the scene tree.
In OOP the ability to store a script can for example be realized by storing what's called a pointer to a data structure representing the script, or even to a chain of such structures. This ability itself can be inherited from the root all the way down, but what is actually connected to this pointer (or whatever method is chosen) can differ.
Like you can have dad being a merry fellow with a blue hat and yellow boots (hello Tom) and his son being more down to earth wearing sandals and a baseball cap :-). Yet still both are humans and one inherited from the other, with different scripts attached for mood and clothing. They even can change their scripts, by changing their minds, but they can not escape the tree of inheritance. Same with OOP inheritance and composition.
Hope that wasn't totally incomprehensible.