Please correct me if I'm wrong.
When a mailbox or ou is enabled for archiving, the policy is tied to the ou. So, the policy applied to a mailbox is completely dependent on the ou it's located.
Allowed - mailboxes in one or more ou's w/same policy stored in different vault stores.
Not Allowed - mailboxes in same ou's w/different policies stored in different vault stores.
SO, bottom line is to apply different policies you MUST alter your OU structure?