I don't think it's misleading at all, the comment you're looking to is.
People really do ask where "The AT Proto server is" as evidenced by this thread, and the really is no "AT Proto server" or "instance". AT Proto and BlueSky are a collection of services with no 1-1 relationship to a Mastodon or RSS server.
The misleading thing is that people asking do not care about the exact construction of ATProto. They ask whether they can self-host and control everything and still interact with the main network.
Regardless, ActivityPub and ATProto have different designs and goals. Your question is akin to comparing a helicopter and an airplane.
There's no such thing as a "ATProto server". How complicated it is, and the trade-offs it made are valid criticisms of it. It all depends on what exactly your goal is as a participant of a distributed social network.
What makes up the ATProto is more than one type of server. Compared to ActivityPub where you just run a single Mastodon instance and you're set.
If the thing you want to own is your identity and data, you can fairly easy run a PDS yourself. If the thing you care about is different moderation decisions, you can run your own labeller (moderation system) or subscribe to another someone else has made.
The answer here would be "there's no such thing as a generic "server" like in ActivityPub because it's split into different components, of which a PDS is only one".
Honestly my main question here is "If you disagree with various ActivityPub instances' defederations, you can get around this by starting your own instance that federates with everything; is there an equivalent for bypassing Bluesky's moderation decisions?"