Fediverse

Ahh, so if I’m on Site A, I can view and comment on things from Site B, so long as A and B are federated with one another.

There's a bit more to it, but essentially yes. For example, beehaw.org has defederated from lemmy.world, but we can still view their content. We can interact with their content and reply to their posts, and other instances that they are federated with can see what we do there, but beehaw users can't see any of it. Basically federation is a one-way street. You can federate with an instance, but they don't have to federate back.

Apart from “don’t affiliate with The Zuckerbot”, I’m still not sure what the worry is all about.

That's kind of the motto of the fediverse in general. It's supposed to be de-centralized and de-corporatized. There are no built-in features for advertising, for example. It's meant to be a place that is safe from the things that we're afraid Facebook is trying to do. Overall, it mostly is. They can attract people out of the fediverse and into their garden which they plan to wall off, but they can't quite shut down the independant instances.