Being centralized isn’t the only reason, but basically yes. The concept behind the protocol is simpler because your decryption keys only ever live on one device. You don’t really have the entire trust (and key sharing) model for devices that Matrix has. Signal’s desktop app works very similarly to WhatsApp where your single main device needs to be connected at least intermittently for “guest” sessions to be able to send and receive messages. I haven’t used Signal desktop though, that was just the impression I got from it. Would make sense though because WhatsApp is allegedly borrowing from Signal’s protocol quite a bit.

It is just closer to WhatsApp. What Matrix does, especially with regards to enabling true multi-device support, is quite complex overall and sometimes causes issues with keys for decrypting messages not arriving on all devices. Signal is more limited but it just works a lot better. Small but important extra: Signal supports fully encrypted voice and video chats.

Full disclosure: I personally also prefer Matrix because I use it with multiple devices. I don’t want to install desktop apps for these services and Element runs in the browser while Signal does not.