No, you're misunderstanding the nature of the Fediverse. The fediverse concept centers around independent servers interconnecting and communicating with each other over activitypub, not all servers everywhere, just simply independent servers (AKA there is room for defederation and bans in that model). There will be servers which choose not to or won't be allowed to interconnect and that isn't antithetical to the goal because the goal is having servers be able to do it. If you were told that fediverse means all activitypub servers interconnect they were either misunderstanding or lying.

The nature of the fediverse is that it's federative/defederative. If an instance chooses to defederate because it thinks federation is a risk then they can do that. If that causes a problem for a user, the user can move to another instance which does federate.

I joined the fediverse after years of bad experiences on more typical social media sites, and specifically lemmy.blahaj.zone instance because the admins are very good at weeding out transphobia. If they federated with Threads I would be very surprised and want them to convince me of why that was a good idea.

People have wildly different ideas about the nature of the fediverse. That's the nub.