[OT; tl/dr: the issues with forums and user accounts being under hegemony of server instances is by design but it’s not actually the way one would design a truely de-centralised network]
It’s a feature but not the best practice if the idea would be forums (and users) being free of domains (and the dangers of domains being taken down, and host admins’ whims). The design approach of Lemmy however, speaks “hegemony” all over. It says a lot about the mindset of its creators.
An alternative would be indeed distributed directory systems, employing concepts like DHT … well proven de-centralized resiliency for quite a while. Would it have been done in such a way, there would be no difficulty with migrating forums and users across instances, and even a domain getting lost would not necessarily lead to all forums/accounts there-on to be lost. Also the issues with link creation across instances were due to forums being bound to domain names instead of them having Universal IDs thus being agnostic of which node they are actually hosted on.
ActivityPub, AFAIK only defines a protocol for communicating datasets between instances, not the structures in which federation should be done.