The migrated mailbox contains a folder called "All Documents" which didn't exist in Notes. What is this folder?
The "All Documents" folder created in Outlook is typically a repository for orphaned mail (mail which does not exist in any view or specific folder in Notes). This is retained because of the "MigrateOrphanedDocs=1" option in the Global Default Settings (INI) file.
To disable the Orphaned mail migration:
For more information on this setting, see the Program Parameters Reference in the documentation.