What you call "fragmentation" is perhaps better described as "multiple moderation philosophies applied to the same topic" and is actually a fundamental aspect of the ActivityPub protocol, which was designed above all else to create platforms that resist centralization.
I'm not saying you're wrong to dislike it, but it is definitionally impossible to have both decentralization and centralization at the same time.
You've taken my words and twisted their meaning to create an antisocial strawman to attack. I will not engage.
That said: if you are someone who views the power instance administrators have over their instances to be "tyrannical", then ActivityPub —a protocol which by designdecentralizes power away from a CEO and into the diverse hands of instance owners— is probably not the protocol for the sort of platform you're looking for.
Allowing Lemmygrad to have it's own "books" community looks like a feature to me, not a problem. The terminally online tend to overpower any other conversation. IMO, we should work to preserve a diversity of perspectives. If all discussions are forced to be centralized we've just recreated Reddit with extra steps.
I am with you as a user, but also an instance administrator. Forcing our hosted communities together with federated communities would take away nearly all motivation I have to host an instance in the first place.
The users who post in the "one big community" are the users who want their posts to get the most views. Personally speaking, I generally do not want to be a part of a community full of those kind of people (with the exception of if I have a tech support question or similar).
Not everyone wants to be in the most popular space, this "feature" essentially forces everyone together. I believe the social web thrives with a diversity of approaches to community structure.
If I'm understanding this "feature" correctly, it feels antithetical to what I view as a fundamental aspect of the fediverse, which is diversity of moderation via decentralization. We came to the fediverse with the explicit purpose of escaping the tyranny of the majority that Reddit forces upon mod teams. This feels like a large step on the path to remaking reddit "with extra steps" and would probably be a deal breaker (for me personally at least).
I think a better way to implement a similar feature, is to give mods an ability to "boost" posts into their communities (with consent from the other mod team to prevent brigading). That maintains the separation while still allowing mods to make exceptions and consolidate comment threads where they deem appropriate.
After all, any instance can pickup some of those and isn’t representative of the instance as a whole.
I think I speak for the whole admin team that we actually do hold instance owners responsible for the communities they host, the same way we hold Reddit (the company) responsible for the communities they choose to host. That said, we made the decision that (for now) the best practice for handling large general purpose instances like .world or .ml is to take a scalpel approach until such a time comes that the Threadiverse is more resilient.
While ostensibly a "general purpose" instance, users on Hexbear had a tendency to come to our hosted communities and aggressively push propaganda, unfairly burdening our mods, so it was a much easier decision to de-federate. We actually did announce that one because of their size.
(Also FYI in case you're not aware you are posting form lemmy.world so just to be clear none of these policies apply to your current account!)
EDIT: I also think it might be useful to highlight that we never take actions against other instances, we take actions for our users/communities.
We're not opposed to hosting non-Star Trek communities as long as they adhere to instance guidelines, but before you move you should know that the federation gap with .world is closing and should be finally caught up before the end of the week.
If we go "by the book" like Lieutenant Saavik, hours could seem like days.
But seriously it will take days.