Do you mean Exchange Provider 2007::MoveMailbox?
This procedure just calls Move-Mailbox cmdlet. So, it does the same as regular Exchange 2007 admin UI, but without any visual response about operation progress.
Your "additional headaches" are same as before in HMC 3.5 - you have to update Resource Manager. Deallocate mailbox in old store, allocate in new one, plus (probably) update owning organization allocations as well.