I think you're inferring something that people aren't implying, and that inference leads to you eventually discussing how ATProto is better than mastodon. I think this doesn't look great, particularly at a time where there's quite a few posts of about unproductive conflict between open social network contributors. I don't think there's any bad intent or malice on your side: there is value in comparison between AT/AP to help understanding.
Your argument that there are no instances in ATProto isn't flawed if you redefine instances as this thing that ATProto doesn't have. But if I run it by the various computer science definitions I can find (e.g. https://en.wikipedia.org/wiki/Instance_(computer_science)) then your argument seems like it depends on a niche interpretation. So it can be technically correct, but just irrelevant or inconvenient when used in a comp sci discussion involving the word "instance".
But your blog post on the subject is interesting, and informative, and has some great diagrams, and the original parent poster agreed and learned stuff from it. Despite that, I think the implication in the parent post was, IMO, "so the main, largest implementer (instance) of the protocol is also a for-profit which owns the trademarks? I never realised that, I'd assume the protocol was governed and run by a not-for-profit independent governance org, charity or consortium" (like some other open protocols).
I think that's a fair and slightly critical implication that has nothing to do with network topology. I completely get how you would want to take issue with that implication alone, because without context like the trademark was acquired with good intent to protect protect openness, and that the Bluesky org is a specific type of for-profit (PBC) that expresses intent to favour public benefit and openness, it makes things sound more sinister than they are.
Ultimately, from an openness and independence position, I think it would be better looking from the outside if the ATProto and trademarks were governed and managed by a separate not-for-profit entity that wasn't tied to the biggest instance/implementation of the protocol. I think that was the point being made, and I don't think it's absurd. But I think refuting that argument by focusing on network topology and instance definitions seems like a misunderstanding somewhere.