While... frustrating to see that these vulnerabilities exist, I'm happy to see that at least the bulk of them require a malicious homeserver.
And Matrix makes it easy(ish... if you're a sysadmin type...) to run your own homeserver.
I've generally assumed in the past couple years of running Matrix that if someone else controlled my homeserver, they could probably do something malicious, which is why I run my own, on hardware I control. Perfect? No, but it's a sure bit better than running on some major tech company's chat infrastructure.
The main problem is I don't know of anything better, short of just giving up and going back to IRC - which, even with znc, isn't nearly as nice as Matrix/Element/etc, though it's far lighter to run at all ends. And IRC is mostly just plaintext (yes, there are some plugins that help, no, they don't really work reliably in my experience with them).
I'm open to being convinced otherwise, but even with this bit of a charlie foxtrot going on, I still think Matrix is probably the least-awful of modern chat options, if you can run your own homeserver.