2FA has never been described as protecting against (1) or (3). That’s not what it’s for; treating these as deficiencies is tantamount to criticizing a hammer for driving screws poorly.

2FA exists to make authentication more difficult for an impostor or attacker. The goal is to prevent account takeover, which has historically been a risk to critical packages in multiple ecosystems.

(2) is sort of ambiguous. I’m not aware of a major case of either TOTP or WebAuthn being compromised en masse because it was on the same device as the first factor. I’m not even aware of a case where WebAuthn has been meaningfully attacked, full stop, despite theoretical breaks of hardware stores. Even with a full break, WebAuthn provides detectability: cloning the factor means cloning the counter, which will alert the user on the next login. On whole, I think it's incorrect to frame 2FA as generally breakable without qualifying the threat and explaining how it applies to PyPI users.