Very first complaint is that one can't tell from imports what is being used or not. If you use a linter that removes unused imports then you can tell.

No. The very first complaint is that if you don't know what is being used or not, you cannot tell whether a new "import" will add _another_ cross-module dependency that did not yet exist.

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.