It's not that different.

Whatsapp controls nearly everything: servers, clients, protocol.

Matrix has open protocols, several implementation of the clients/servers, and people can start their own server node.

In the comparison to TCP/IP this is quite similar. You can add to the network without needing approval of a central institution.

But Matrix works fine if a hospital disconnects itself from the internet because of some DDoS or hacking attack. WhatsApp doesn't, because you can't host it on-prem. I am not sure about if governments have that use case, but we certainly have seen it in hospitals. (And even then, there are benefits of having patient data only on specific servers in specific environments, even if they are encrypted, because if you use WhatsApp to talk to your doctor, Meta will know about that. And I am pretty sure governments can appreciate such features as well.)

>This is a different type of centralisation, though

Not really. There's a single entity that controls WhatsApp and so the entire service can be stopped by threatening/sabotaging that single entity.

It is the centralization type that matters.

Obligatory reminder that the whole "Internet routes around censorship" like it routes around glassed data centres during nuclear war, etc. applies to layers 3-4 of ISO/OSI model. The problematic centralization of the Internet happens at layer 7.