Calling Matrix decentralized is a little misleading. If's a federated protocol that still relies on user-trusted "home servers". Currently the majority of folks use the `matrix.org` home server, but a number of other folks (like myself) operate their own home server.
This means if a user on the matrix.org server is talking to another user either on matrix.org or elsewhere, matrix.org (and the 'elsewhere' participant's server operator) will be able to determine who is talking to who.
Also of note is that e2ee is optional, which makes sense because Matrix isn't just a replacement for direct user to user or small private group messaging, but also large public groups, where message content is intentionally public, and e2ee just adds overhead.
This means if a user on the matrix.org server is talking to another user either on matrix.org or elsewhere, matrix.org (and the 'elsewhere' participant's server operator) will be able to determine who is talking to who.
Also of note is that e2ee is optional, which makes sense because Matrix isn't just a replacement for direct user to user or small private group messaging, but also large public groups, where message content is intentionally public, and e2ee just adds overhead.