Type stubs for single-file top-level modules

PEP 561 currently states the following:

Package maintainers who wish to support type checking of their code MUST add a marker file named py.typed to their package supporting typing.

I consider this requirement to be problematic for Python libraries that are written in another programing language and distributed as compiled .so files. PEP 561 currently does not provide a way to mark .so files residing directly in site-packages/ to be typed, resulting in typed shared libraries needing to introduce an intermediary __init__.py file such as the following:

from ._native import *

__doc__ = _native.__doc__
if hasattr(_native, "__all__"):
    __all__ = _native.__all__

While this works for static type checkers I think this is obviously suboptimal because it has several undesired side-effects. Let's take the following as an example:

site-packages
├── my_project
│   ├── __init__.py
│   ├── _native.cpython-36m-x86_64-linux-gnu.so
│   └── py.typed

The unintended side-effects are:

1. You can import my_project._native.
2. _native shows up in the documentation generated by pydoc. E.g. under PACKAGE CONTENTS for the documentation of my_project and invoking e.g. help(my_project.foobar) will tell you that foobar resides in the module my_project._native.
3. my_project.__file__ now is the __init__.py file instead of the .so file, potentially misleading developers into thinking the package is implemented in Python

So I really think PEP 561 should be amended to provide some way of marking single-file packages as "typed" without having to resort to hacks such as defining an intermediary __init__.py since that introduces a bunch of undesired side-effects that have the potential to confuse API users.

What do you think about this?

Start by reading PEP 561 and the issue's examples of single-file compiled modules, then compare the stated behavior with how pydoc reports package contents and file. Done means proposing and documenting an accepted way to mark directly installed .so modules as typed without the intermediary init.py side effects.