You've painted MBM in pretty glowing terms. A great deal of potential downside. If there were not, many more medical schools would have implemented MBM already. Let us just indicate to you some of the more obvious ones. First, the mission-specific accounting exercise that is part of MBM often yields surprising revelations.
Schools find that some missions cost less than they had assumed, while others cost more.
This can have an unsettling feature if certain revenue streams are premised on the original assumptions. As mentioned before, the act of measuring something implies a value statement. It promotes behavior intended to produce the outcome being measured. This, of course, is the purpose. But the measurements can have unintended outcomes.