Reading through the Pull Request, it's nice to see such a civilised, courteous dialog between the submitter and maintainers (https://github.com/python/mypy/pull/2761). I can imagine (and have previously seen) many similar dialogs break down and resort to less errm... "empathetic"/productive comments. Guido++!

Yep, until we eventually move everything into `pyproject.toml` which is explicitly documented to support `[tool.foo]` config namespaces.

https://www.python.org/dev/peps/pep-0518/

That's explicitly called out by miedzinski, the PR author, in the discussion [1]--although for some reason it's mentioned as PEP 512 but links to the same page you mentioned.

[1] https://github.com/python/mypy/pull/2761