Warning "duplicate object description" if class is in too many `__all__`s, when using `sphinx-apidoc -e`

[KendrickLamarck]

Describe the bug

I get WARNING: duplicate object description of [...], other instance in[...], use :noindex: for one of them If

1. A class is included in two __all__s which do not belong to the module where the class is defined,
2. sphinx-apidoc's option --separate/-e is used.

This is not a problem for functions, only for classes.

How to Reproduce

Minimal method:

Say you have a directory structure

.
├── mainpackage
│   ├── __init__.py
│   └── subpackage
│       ├── __init__.py
│       └── module_in_subpackage.py
└── docs

With the following file contents:

mainpackage/subpackage/module_in_subpackage.py:

class MyClass:
    pass

def my_func():
    pass

mainpackage/subpackage/__init__.py:

from .module_in_subpackage import MyClass, my_func
__all__ = ['MyClass', 'my_func']

mainpackage/__init__.py:

from .subpackage.module_in_subpackage import MyClass, my_func
__all__ = ['MyClass', 'my_func']

Now run, in .:

sphinx-apidoc -F -e -o docs/ mainpackage/
PYTHONPATH=/absolute/path/to/./:$PATH make -C docs/ html

You should get the warning, but only for the class and not for the function.

This example can also be found on my github at https://github.com/KendrickLamarck/sphinxbugtest.

Environment Information

Platform:              darwin; (macOS-12.6-arm64-arm-64bit)
Python version:        3.10.8 (main, Oct 13 2022, 09:48:40) [Clang 14.0.0 (clang-1400.0.29.102)])
Python implementation: CPython
Sphinx version:        5.3.0
Docutils version:      0.19
Jinja2 version:        3.1.2

Sphinx extensions

['sphinx.ext.autodoc']

Additional context

No response