"Who's CEO" is good shorthand for "do you know who's responsible for what kind of decisions?"
IMO, it's much more efficient if each individual focuses on his domain and provides a single interface for the stakeholders for that facet of the enterprise.
The overhead of communication and context synchronization become ginormous as the organization grows and the issues affecting the enterprise grow in number if every decision is made on a flat basis. If the context synchronization is not made then the decisions made by the group will be less informed than that of an individual. For informed decisions, it would require then that each individual become an expert on the single issue discussed. This would effectively negate the main benefit of small teams - individual focus and small communications overhead.
This is not to say that flat organisations are bad. But I don't think they are a particularly good fit for the scale YC companies work at.