Throughput accounting measures the value added to the business, process, or entity by virtue of project accomplishments
Value added is only measurable as an accomplishment, presumably an operational difference in the business, process, or entity that makes a meaningful difference. In effect, what is being measured is how much more valuable is the entity now than before. If expenses are lower, than the business is a more valuable transformer of revenue into profit. If a public sector mission is more effectively accomplished, then the entity is a more valuable contributor to public "welfare".
Value added is a "difference calculation"; in EVM terms, it's a variance. The absolute values of each factor in the difference are less important that the difference itself.
So, what's not accounted for in this variance calculation? Answer: operating expenses [OE] of the project...expenses traditionally called 'actual cost' [AC]. Why exclude AC? The idea is that PMO's and project shops, particularly IT shops, have more or less fixed operating costs. If not this project, then some other will absorb resources. Also, most IT projects involve contributions from non-IT sales and operations staff that are 'fixed costs'. Unless there is some direct incremental expense, like a special tool or facility, or a direct contract for services...like a consultant...then the day-to-day OE of the project is not included in the value difference. If there are such direct and incremental expenses, then they are included as part of the value variance.
The figure below gives a pictorial of this idea. "A", "B", and "C" refer to different projects