PyPI and pip are both under the "umbrella" of PyPA, but they're separate projects with (largely) separate maintainers. The audit was only scoped to the former, not the latter.
(FWIW, I don't think the security posture of pip is obvious to everyone[1], and I do think it would benefit from a separate audit!)
Does it matter if the code-execution happens at `pip install` or `python myapp.py`? Using 3rd party libraries inevitably means you're allowing code-execution to 3rd parties, that's the point after all.
Replace "manually read through every file" with "run your security code scanner against every file" and it becomes less nonsense, but just as applicable.
In reality this really isn't how code scans are done, so it's still a little silly, but I could theoretically see something like this being a desire.
(FWIW, I don't think the security posture of pip is obvious to everyone[1], and I do think it would benefit from a separate audit!)
[1]: https://yossarian.net/res/pub/hushcon-west-2022.pdf