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I get why Federation can cause issues (most of the time it's moderation related), but why would an extra option be a deal-breaker? Federation can always be disabled on a per-domain basis if you prefer. In fact, I'd argue it's best practice to only allow domains on a case-by-case basis to prevent spam and abuse.
On the converse, you can't enable Federation on a platform that doesn't have it.
They were talking about matrix itself, not a specific option. And I’m not going to lie, having to hand hold your servers federation choices seems like a hassle. At that point why not just use a self hosted, non federated option?
I think the point they're making is you can effectively have a self hosted non federated option with Matrix. Just disable federation as a whole (which I'm pretty sure is completely possible. Given companies use matrix for comms, and might not want federation, for similar reasons to what is being discussed here)