I agree that this particular scenario is not immediately intuitive. But think for a moment if Internet senders/recipients were not held to the global limit. What about the scenario where a particular relay is allowed -- for example an Internet user is sending to a contact in your organization (that exists elsewhere) or even a non-authoritative domain (which doesn't require a contact object). In this case, it would be difficult for us to determine the administrator's intended size limit if the globals did not equally apply. I'll be happy to take suggestions of how to handle that type of case -- perhaps we could only apply the limit if the domain is non-authoritative and the recipient is not a mailbox? Problem is that just makes it more complex...
Your scenario is easy to achieve by doing the override in reverse -- set everyone's limit lower than the global except for the CEO. With the Exchange shell, this is easier than ever.