It’s less about the separation of powers and more about the fragmentation of each power. As in, you should be able to ditch any governing power that you dislike, and curb down its influence on your experience to a bare minimum.
So perhaps the best analogy with RL politics would be a confederation with lax citizenship laws and federated entities being free to choose which other federated entities they interact with. With a key difference:
The Fediverse can be completely acephalous. And the reason becomes evident once you analyse the UN of your example - it’s effectively Europe and USA wearing a bunch of sock puppets, pretending to talk in the name of the “nations” (actually countries, but whatever) of the world. An acephalous Fediverse would not develop a similar problem.
In this case (Threads), it means that, while we should promote defederation, how to deal with it should be, ultimately, up to each instance.
NATO example
I don’t pay taxes to any NATO country so what I’m going to say is solely based on the Fediverse situation, plus whatever I parsed from your example:
We should not need to rely on “trust” on first place. Instead a better approach is to acknowledge that people will fuck it up, they will do things that counter the best interests of the whole, and that the system needs to handle it.
For example through a ActivityPub commitee that exists anyways or a popular meetup of Fediverse servers.
What happens if said commitee becomes hostile, defending its own self-interests in detriment of the ones of the rest of the Fediverse?
I think its good that different moral rule sets can easily develop and implemented; but I think sooner or later it will become a problem, at the latest when more radical parts become pre-dominant.
Or we could leave those moral matters up to each instance to decide. And the ones screwing up on moral matters get isolated.