I completely agree on the first two paragraphs.
Wrt. signing: I'm assuming we are talking about PyPI and NPM here. Also I'm assuming the major threat vector for a repository compromise is that (some of) the dev's accounts on some other services (most likely email) are somehow compromised. In which case it's down to that dev's OPSEC practices whether the repository can be compromised using the data from $OTHER_SERVICE. If the dev has poor OPSEC and would reuse the password for multiple accounts in a user/pass repo auth scenario, it's reasonable that this person would also have emailed themself the keys for signing packages, e.g. for transferring to another location behind a firewall. In either case, you're down to trusting the dev's OPSEC.
IMO, the threat models for other kinds of compromises which signing protects against are much more far fetched. AFAICT neither PyPI nor NPM use third-party mirrors, which basically leaves MitM attacks. If an attacker is capable of successfully MitM-ing the connections you make to PyPI/NPM over https, you have much bigger problems.
Or am I missing your point here?