I don't think the article talks about unused dependencies anywhere, does it?
As I already mentioned in another comment, you have:
.../module1/__init__.py -> import module3
.../module1/foobar.py -> import module3
.../module1/baz.py -> import module2
Now you are editing or reviewing a change to foobar.py. How can you tell if depending on module2 is conceptually OK? You need to look at baz.py to prove to yourself that the dependency already exists. Or you need to know a priory that it's an OK thing to do.