In that essay, I (we) were thinking about moderation primarily in terms of users: what content they see, who else they can interact with. Not so much who runs the underlying services or networks themselves.
You're right, of course, that if you disagree with the people running a given instance or network, you should be able to choose not to use it or have your content federated into it. The mechanics for that are generally much simpler: users and admins can just block eg the threads.net and/or bsky.brid.gy domains.
Even putting aside Threads and Bridgy Fed, though, this does reiterate one of the essay's points. Federation itself in the fediverse is generally opt out. Most instances don't start as islands and deliberately choose who to federate with; they start out federating everywhere, even with corporate instances like me.dm and flipboard.com that they might have issues with on content handling grounds.
This is one big area where @jdp23 and I agree: opt-in federation (aka consent-based) may be the better approach for at least some people.