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I understand the benefits from instant web chat, but I think it's not too difficult to access the signal protocol through Whatsapp or Signal's desktop app.

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Those implementations both require phone numbers and registration through a mobile app (hence lack anonymity) and are useless for many use cases.

I think Matrix (Riot) would be a better choice. It's e2e encrypted like Signal but doesn't have any nonsense reliance on phones or phone numbers. It also has extra features like true multiple device support, a federated protocol and an open server implementation.

And what is the use-case for this? I probably somehow miss it.

same reason you would host a gitlab or github enterprise instance instead of using github.com, only this time applied to encrypted messaging

https://signal.org/blog/whatsapp-complete/

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