Earlier quoted context omitted.
It's one of the most significant open source messaging systems that exist today. Anyone can audit it at any time. What more do you want?
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."