The difference between a password manager and TOTP is that TOTP is something PyPI can enforce and a password manager is not.
Yes, TOTP adds very little advantage when you have an already safe password. But there is no way for PyPI to know if you're doing that or not, and they can know if you're using 2FA.
> 99% of people affected by this mandate (and 99.9% of 2FA users in general) are going to use an implementation with these weaknesses
Time will tell. PyPI is giving away free keys, presumably to encourage adoption of the safer option.
I'm actually very happy to see maintainers go. If they weren't willing to enable 2FA I worry about what other issues their software poses.