"A federated protocol is a protocol (defined next) that makes it possible for servers to communicate with each other, regardless of who is running those servers."
Federation implies delegation from a central authority, which makes Mastodon and ActivityPub more “confederated” than anything. Inasmuch that MX records stem from the root servers, email is federated that way, but otherwise it’s decentralized, with every MTA being its own authority. The line is fuzzy.
I think it's important to distinguish between application layer and lower layers of the stack here. For the lower layers (firmware updates for protocol changes notwithstanding) it is basically all federated, as you say. But at the application layer there are protocols that you can participate in just by knowing the protocol, and others which require knowing a secret or getting included in trusted peers or otherwise filtered to effectively make them proprietary and not federated.
It is decentralized