Recovery Manager for Exchange will export all items from an Archive Manager mailbox that are linked to folders in that mailbox.
There could be items linked directly to the root of an Archive Manager mailbox which are not linked to folders and these items will not be exported by RME.
The items linked directly to the root have been associated to the mailbox because the email address that is assigned to that mailbox appears on the To, From, CC, or BCC field of the message.
These items linked only to the root were never found in the users mailbox by Archive Manager, but were added to the archive in another manner. That other manner is typically Exchange Journaling or users dragging the contents of a PST file into their Exchange mailbox.
None.
This is by design of Archive Manager. Recovery Manager for Exchange will export all items from an Archive Manager mailbox that are linked to folders in that mailbox.
If you expand the Mailbox in Recovery Manager for Exchange or Archive Manager and count all of the items at the Inbox level and each Folder level you will notice it is equal to what was exported.