The article says that "Godot does composition at a higher level than in a traditional ECS", but I don't get what he means by that? Combining nodes with incompatible hierarchies is hardly composition, and is just what you typically have to do when using inheritance.
Inheritance-based entity systems are not always terrible, and even though I tend to hate them, I use them quite a lot in my projects where an ECS would be overkill. If designed for a particular project, you can usually be more productive, and write cleaner and less code with inheritance.
However, for a general purpose engine like Godot, that's a bad choice IMO. The flexibility offered by an ECS far outweighs all benefits of an inheritance-based system.