An external message is counted differently depending on the Exchange version and the perspective (i.e. Server versus Mailbox). Here is the breakdown of those descriptions.
On a server report, a message is counted as external when the message is sent to or received from another server that is not an Exchange server in the same organization. MessageStats is aware of what servers are in the given organization and check messages that are coming in or going out.
On a mailbox report, a message is counted as external if the namespace in the recipient is not contained in the Internal Namespace list.
On a server report, a message is counted as external when the message goes through the IMS. For Exchange 5.5, there is an Event ID corresponding to sent and received messages through the IMS. MessageStats looks for these particular events.
On a mailbox report, a message is counted as external using the same reasons as for Exchange 2000/2003. In Exchange 5.5 tracking logs, internal recipients are quoted using its distinguished name and not an SMTP style email. Therefore, it uses this check along with the Internal Namespace check to see if the logical message is external.