Turns out that when you set the NuPoint to MAPI, the NuPoint doesn't really do anything different with the message. It actually still sends it as IMAP, however it lets you specify up to 6 MAPI Gateways, which is Mitel software installed on a separate Windows machine living on the same domain as the Exchange server with a superuser account with the right permissions to send to the Exchange server. The MAPI gateway converts the inbound IMAP message to MAPI, thus now making it readable by the BES (i.e. headers, etc.).
So the bottom line is that you need a separate Windows machine to make this work. Supposedly it is because MAPI cannot work in a Linux environment due to its proprietary Microsoft nature, so Mitel can't embed it in the MAS/NuPoint.