The fact that every instance is capable of being its full-fledged thing, doesn’t mean it has to do so. That’s why we have federation. So yeah, federation allows any approach you want, like the one you mention, of having instances that focus in certain topics, but having generalist instances is okay too. The important part is that users from one instance can participate in the communities of other instances.
I, for one, came here for a reddit alternative, and not having general instances would be a huge turn-off for me personally.
Every instance has sort of a theme of its own, but since most instances are federated, that doesn’t really make a difference: the entire federated network is the Reddit clone.
Each instance should look to have an identity/define what is it about, from there its a moderation challenge. If there is a instance better suited for a community, in a perfect world it would be possible for mods refer them there, but regardless there will always be some kind of general content / pull to stick to one server as thats how some people work.