Answer:
By default, our tool will only migrate Mailbox Folder Permissions for System folders. To migrate permissions on folders that were created by users, the Advanced Option must be set to MustMigrateAllPermissions=1 in your project.
Notes:
This setting is an option because it is not a best practice, and scanning for the permissions will slow down the migration.
We do not migrate any permissions for the Default or Anonymous user accounts.