You hold viewpoint A and claim that those that hold viewpoint B do it because they are mad because they don't get their way instead listening to the actual stated reason, such as OPs.
I think federation is absolutely interesting but this is definitely a consideration and pretending everyone that raises is "umad" or bad is not compelling. Communities online already have problems of "circlejerk" and extreme uniformity. This could easily foster that even more to a point where there's really no communities of significance. Just similar things to 20-100 people using a chat medium to share stuff.
Just read your post and I get its points. I don't see how combating one misrepresentation with a misrepresentation of your own improves the situation but at least I get what you're aiming to respond to now.
Even if you don't think it as ideological, there's some functionality/existencial aspects that make a discussion interesting. Instability and arbitrariness, if there's a lot of change without consistency and transparency, can lead to only people who value the authority's opinion.
In a way I'm trying to decide if in practice instance federation works like "this is my ball, and we'll do what I say when I say, and you accepted that because it's federation" or if there's a more open promise for stability. How much deep the fragmentation will go because of disagreements and how much friction does that cause on the end users when this happens (this is something you talk about when you mention the Identities across instances)
Maybe it's less prone to change and can provide more stability but an event like reddits current situation definitely brought about some chaos.
The mod post about talking with the other instance admins seems like it's not about animosity but amicably spoken ideological differences but that goes back to my point.
When something is so exclusive maybe it'll have to invest extra to not be misunderstood when it's shared often with a different pitch, using more centralized patterns that are known to "mainstream" social network/forum users.