Since the entire goal of the fediverse is “transporting” all data to all servers inside the ActivityPub/fediverse world, the data of a EU member will be transported all over the place.
Not all data is transferred to other servers. That's the point where I think you are wrong.
You mention email and IP addresses as examples of personal data covered by GDPR, but that data is not transferred to other instances, only the instance where you registered holds that data. So you would only need to care about the instance where you registered to be GDPR-compliant.