Archive Folders and Personal Folders are not part of the Mailbox.
When you receive messages, they're sent to the Inbox. Typically, the Inbox is stored inside the Mailbox, along with Calendar, Contacts, and other folders. When you store messages locally, you send them to Archive Folders or to Personal Folders, separate data files that are outside the Mailbox. Outlook knows where to find them, but the server doesn't count them against you.