Which features do you mean? Not disagreeing with you, I’m just curious.

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.

There is no single keychain on Linux, and supposedly on Windows too. Signal would need to either support a few dozens of password managers or require a specific one, both options terrible in their own way. This isn’t something that can be done without making broad assumptions about the user’s system.