After reading your comments on the LibreSignal tracker, my impression was that you are very much writing with your business hat on, as you are framing alternative clients as "products" and trying to protect the Signal brand, as well as preventing third-party clients from using your service - all typical business moves.
I can see how federation breaks the phone-number-based identity and discoverability, so I accept your position in that regard.
However, opening up the service to community-developed clients would be A Good Thing. You have to maintain backward compatibility to a certain degree for the official client anyway. If community clients fail to roll out a new protocol version, it will be a valid move to lock them out together with outdated official installations. You wrote that maintaining servers is difficult, but I am sure that it is possible to find a scheme where your additional financial burden of accepting (but not providing support for) third-party clients is compensated for.