The Fediverse is bigger than just Mastodon, so it's more the other way around. :)
The way I understand it, there is one fediverse and Mastodon instances effectively are connected to a subset of it (primarily by blocking out the bits they don't want to interact with). In principle groups of instances could form their own separate federation groupings, but I don't know to what extent that happens (if at all).
At the begining, the fediverse was not that complex, and very much some open source people and some nazi, with a sizeable overlap.
Mastodon arrived and eventually added more protocol. It was driven by minorities and other people that were getting shadowbaned etc. from birdsite and also open source people.
The moderation tool such as blocking instances allowed admin to make value based judgment.
In the past blocking instances was just hidding stuff. So a blocked nazi instance would still see the content, comment and reply, just the blocking instance(s) wouldn't see it
Of course it is not what is needed.
Eventually an authorized fetch option was introduced so blocked instances would get no data at all, stoping them from seeing and interacting at all.
It is now looking more like clusters, of very close instances, and some link between big instances, mostly because they get more connection to more other instances by virtue of having more people.
So 1 fediverse, many protocol, and many cluster that continue to define themselves as time goes on.
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