Then why are instances defederating whole instances if they’re unhappy with the content of specific communities?

Because on a public instance with many users, any single user can put the URL to a community in the search bar and start the federation. Then it will start showing up on that instance’s “All” tab. If I go to lemmy.world right now and use their search bar to search for someweird.instance/c/among_us_porn, everyone will see those posts on “All.” Based on the name, most people probably don’t want to see that, so they’d be tempted to defederate.

Also, accounts belonging to users on other instances can comment on any public post on any instance, provided they haven’t been defederated. So defederation targets belligerent user accounts too.

What about new communities? Do you need to manually federate with need communities on an instance? This seems like a hassle… How does e.g. lemmy-world do it?

If you’re running a fresh new instance for yourself - yes. Larger instances like lemmy.world don’t have this problem because it only takes one person to start federation. If that one person starts it, every other user will just see it as another community and it will be pretty convenient.

Federation isn’t that complicated though. You just pop the link to the community in your search bar and you’re done.