>How do you know the matrix.org server or the element.io web client is running the same code as the source posted publicly? How exactly do you, personally, audit a hosted service? The answer to both questions is: you don't.
And I don't use them. I grab the posted sources and use them on hardware I physically control. If (I'm not, but I do care about my privacy) I was someone that was being pursued by one or more governments/well-funded private actors, I wouldn't use any communication platforms hosted by others.
As the old saw goes: "Three can keep a secret. If two are dead."