Travis, might want to clarify what is a "business unit direct application".
I came across something that may be related last week. Applications that are "supported" by business units outside of IT. The type of support I'm referring to is application functional support, critical for the App to be of value. Presenting an application TCO excluding these activities would be misleading, but the resources are not part of the IT organization.
The direction I'm taking here is to add a new type of expense (my TBMA is thinking about what this is), an estimate of the cost of that support originating from outside of IT. Note this will be an estimate, and lump sum. Clearly labeled in the TCO reports as such.