Because the keys aren't directly coupled to server configurations, but rather indirected through a CA which hosts the only durable key, those "private keys" users have to have can be extremely short-lived, and tailored for each individual access request.

I think people really get into trouble with SSH certificates trying to reason about the properties of certificates versus SSH keys versus passwords. The format isn't the point; making the endpoint keys dynamic is. If you built a secure messaging system that propagated one-time-use SSH keys, it would address the same problem. Nobody will, because certificates are easier and already work, but you could.