"If you believe in federation as a concept, then it shouldn’t matter how big an instance is. "
That's the opposite of the truth.
The more a particular instance dominates the network, the harder it becomes to defederate from it because so many of the connections people have will lead to that server.
"anti-mastodon.social animus is driven by dislike for Eugen"
No, that's not the case for me.
"Mammoth is actually doing this."
VC funding has always ended in disaster.