Relax `ignore-missing-imports` for modules that have stubs now and update mypy (#11006)

Updating mypy past version 0.9 means that third-party stubs are no-longer distributed with typeshed. See http://mypy-lang.blogspot.com/2021/06/mypy-0900-released.html

 for details.
We therefore pull in stub packages in setup.py

Additionally, some modules that we were previously ignoring import failures for now have stubs. So let's use them.

The rest of this change consists of fixups to make the newer mypy + stubs pass CI.

Co-authored-by: Patrick Cloke <clokep@users.noreply.github.com>