Is there a difference between the Manage My Mail whitelist and the IronPort safelist?
No, they are simply different terms for the same thing. However adding things to the whitelist via Manage My Mail will add the same entries to the safelist on all mailboxes for the selected domain (or for all your domains if Apply these settings to all of my domains is selected). If you add entries via the IronPort interface this would work on a mailbox by mailbox basis.