I think it’ll take a little while to settle down, but I’d expect the communities to congregate on more permissive, well federated servers. In the short term I’m doing similar to you what you proposed, e.g. having accounts on various servers, but I expect the need for this to go away as things settle down. I already focus on a couple of instances more than others.
I do think that less permissive instances will still thrive though, although maybe not so much for general content. That may change as more granular controls and better tools emerge so it’s less of an ‘all or nothing’ approach to federating.
Yeah, it’s not immediately obvious what the implications of an account on a particular instance are. I think over time it should become more obvious, for example meta data about instances on lemmy instance directory sites, so users know what they’re signing up for. I also think things will settle down as communities find an instance that works for them, and tools improve for more granular control over federation.