I can't think of an any with independent implementations.
For instance, have a few third party Signal clients, which work by using the official libSignal . These are not third party clients, but third party GUIs. Use of libSignal on the official Signal network is also not supported or recommended.
Likewise, all the third-party Telegram clients I know of are forks using Telegram source.
This makes sense, because neither of these are stable systems. A third party has to stay up-to-date with features and changes made to the official servers and clients.
Do you know of a security and privacy focused messaging platform which is both:
1. documented
2. has multiple independent implementations of the networking and security protocols?
Security wise, there is interesting work adopting MLS (and I believe key transparency) under Matrix, see https://arewemlsyet.com for example.
That's like saying the internet protocol is neither private and secure because people willingly use random public Wi-Fi
Or put another way: If the privacy and security of imessage is compromised by someone building another client, I'd argue that you never had either to begin with.