Matrix allows for unencrypted messages so it's inherently less encrypted than Signal. The federation capability also means messages leak metadata. Furthermore, encrypted messages also contain some metadata in the unencrypted envelope. Some protocol features (emoji reactions) also ended up outside of the encrypted envelope because of that. It's a risk with any protocol that has encryption bolted on and optional.
On the other hand, you can host your own Matrix server and still participate in the network, whereas Signal will have you convince your friends and family to install a custom Signal client if you want to run your own Signal server, for instance because you don't want to rely on Amazon's servers (Signal was down when Amazon went down this morning).
Signal sacrifices network openness for encryption capabilities.
There's also the MLS/MIMI side of things, but AFAIK that work hasn't been completed yet (MIMI isn't even a full RFC yet).
Element/Matrix, with some modifications, has been chosen as the messenger of choice by the French government (Tchap) as well as the German military (BwMessenger, BundesMessenger) and healthcare (TI-Messenger).