Does the pfdavadmin tool give the option to audit permissions for ALL mailboxes, or is it just one mailbox at a time? Also is the tool reporting permissions granted via delegate rights or those set via AD?

For the first question, yes it can give the option to audit permission for all mailbox. Just select All Mailboxes when you try to connect a Exchange Server. For the second question, not very sure what do you want to know. But with this tool, you can verify the existing permission on user's mailbox, it cannot tell who set up the permission. Fiona Liao TechNet Community Support