We're fixing this by working on P2P Matrix (as per the blog post - it's one of the main initiatives that the funding is going towards). https://matrix.org/blog/2020/06/02/introducing-p-2-p-matrix explains how P2P addresses the metadata problem.
The whole "heavily sponsored by the intelligence community" thing is a conspiracy theory. It's true that Matrix is popular with government and national security folks and Element gets money from them... but it's because they want the E2EE and data sovereignty for themselves, rather than because they are trying to torment their citizens(!!)
It seems like the connection to Amdocs and their interest in collecting metadata for surveillance is a stain on the privacy-focused image.
Now it is too late to rethink the design to be less of a honeypot. So the only solution is P2P matrix. But even P2P matrix will need some way to back up the metadata so it’s saved between sessions. So again the honeypot seems unavoidable.
The tone of the part about connections to Israeli intelligence doesn’t read as “anti-Semitic” to me, as it’s pointed at motivations of the government spy apparatus and doesn’t make generalizations about Israeli or Jewish people. Though the tongue-in-cheek sarcasm is hard to untangle.
The overall tone is sadly that of someone who has spent too much time making internet memes, but I believe the author is a trained linguist with a sardonic sense of humor.
I love Matrix, it is actually my primary chat network. But the way these features are getting added makes me really disappointed. You don't make a secure protocol by stuffing as many features as you can then adding encryption later. You build a secure protocol by making sure that every feature added is secure from the start, otherwise it is rejected or needs to explicitly justify why it can't or shouldn't be made secure.