maybe try setting up a matrix bridge if you feel confident you can secure that properly. On one hand it might increase attack surface (use only servers and bridges with End to Bridge Encryption) but what's an attack surface on software that is so ridiculously compromised. Also you can try using an alternative client such as Flare. Though YMMV, for me the last time I've used it it was quite rough around the edges but I'm happy to see it's actively maintained so might be worth checking out.

Also no, flatpak doesn't fix this issue. Yeah it provides some isolation which can be further improved with flatseal, and other defense-in-depth methods. But unless you are willing to face the trade-offs of using Qubes, you won't compartmentalize your entire system. The key file in question is stored in ~/.local/share. I'm not denying vulnerabilities in userland applications, but thanks to it's wide reach, often massive codebases and use of unsafe languages like C, it's the core system or networked software that is the most common attack vector. And that doesn't ship and will never ship via flatpak.

The most obvious way this is exploitable is directory traversal. But not only that. Just look up "Electron $VULNERABILITY", be it CSRF, XSS or RCE. Sandbox escape is much easier with this crap than any major browser, since contextIsolation is often intentionally disabled to access nodejs primitives instead of electron's safer replacements. Btw Signal Desktop is also an electron app.