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I guess the issue isn't that bad, since the packages aren't pulled automatically (by default), and presumably one would look at the packages they're installing. NumPy specifically seems to provide stubs in the official package, so you should never need to install types-numpy.
code that builds a set of missing stubs
I have a feeling this is an edge case in how the numbers tower works (unlikely) or I don’t understand how the type hints work for int: https://github.com/python/typeshed/blob/c601d5cf3d8968f3dc1fe792bc1da5b43c6a9ed9/stdlib/builtins.pyi#L169