Replies to threads from thread-unsupporting clients are the one potentially-hard thing federation-wise, as doing it properly would require the server to trace back the reply and from that handling it as in the thread, but that's not far from what servers already have to do with edits. Or you could also just not require/suggest that behavior, having replies without thread metadata always be outside of threads; would probably save on confusion too, as the illusion would break anyway when someone on a client without thread support would not do a reply on some message after having used replies on others.
There might be some graph core to it, but it's still primarily a messaging service. Opening the client spec will show you tons of messaging-specific APIs.
I utterly disagree that saving a half-dozen lines in largely-useless toy clients is worth making more feature-complete clients more complex, and doubling the size of every edit event.
Doesn't "some messages are missing" trait defeat the point of a reliable communication protocol?