This is a bad article that is unnecessarily fear mongering about a decent communications protocol. A distinction must be made between matrix.org, Element (Riot) and the Matrix standard & protocol. This article is pointing out some correct issues with matrix.org and element but not the matrix protocol.

matrix.org is the official website hosting the main instance of matrix run by the creators of the protocol.

Element is a Matrix client made by the creators of Matrix.

Matrix is an open standard and protocol not a piece of software, it is decentralized and self-hostable. If a person has issues with the official instance hosted by the creators of Matrix on matrix.org, they are free to choose any different instance. I personally do as well, it is a legitimate point to not use the main instance as it demotes decentralization and ultimately privacy.

While the protocol was made inside an Israeli based company. The funding for the core developer team which worked on it was cut off and they found a new company in the UK. Evidence for a mossad relation are slim but these are not concerning because Matrix is an open source protocol and anyone can audit it and fork it if necessary.

As for Element, there are many other clients for Matrix which do not use Electron. Usage of Electron itself does not make an application non-private. Alternatively you can also use forks of Element like Schildichat.

I will reiterate that the article is targetting the official instance and website of the developers. The actions of the developers on their website does not scruitinize the matrix protocol or undermine the privacy that it provides. Users are free to, and recommended to not use matrix.org.