Either multiple different keychains or even you can have no keychain-like application in your system at all.

The WiFi passwords are usually stored in /etc/NetworkManager as plain files. Granted, they are not accessible directly by non-root users as they are being managed by the NetworkManager daemon, but there is nothing generic for such a thing. Signal rolling a similar daemon for itself would be an overkill. The big desktop environments (GNOME, KDE...) usually have their own keychain-like programs that the programs provided by these environments use, but that only solves this problem for the users of these specific environments.

To me it's perfectly expected the Signal encryption keys are readable by my user account.

Because a non admin account is the default right? Right?

I'm cool with non-biometrics.

(Though "3fa" and "could also" does imply he meant to use all three in concert, but that "just one" would be better than none.)

But that can be said of any of the other such called factors:

A yubikey can be stolen

A fingerprint can be scanned and distributed

So its not really an argument against passwords (or passkeys, or passwordless, or whatever marketing want to call them these days).