Unity uses Exchange 5.5, 200(x) or Domino for it's message store - it does not use it's own proprietary message store and then synch it to the mailboxes in question - the messages originate there.
You need to point Unity at an Exchange server that will act as our "partner" server - we need to be able to log into all mailboxes for message retrieval and message notification functions and be able to create mailboxes and directory (in this case AD) accounts.
This is true for VM only as well as UM. If you plan to use an existing Exchange installation as your VM platform that's fine but you'll want to create users that are hidden in the address book (4.0(3) has this on the profile page for subscribers in the SA) such that they don't show up in the email address books of the desktop clients... you don't want VM only users getting normal emails that they can't retrieve - it'll just clutter up their inbox.