I have a question and a comment. The question first:

Is the cost per square foot fee mentioned in the article for Enhanced Cx intended to represent a cost to do both, or just the added cost to do Enhanced? I am also curious what part of the country this fee is being obtained.

My comment:
Regarding the matrix graphic included in the article, Cx professionals typically do not perform the functional testing, though they may find themselves demonstrating how to do parts of a test to a installing contractor, if it has some particularly difficult requirements. They will typically verify the functional testing, once it has been initially completed by the installing contractors. This verification is usually done by witnessing a repeat of the tests, and in some instances directly participating in measuring the outcomes. The leading members of the committee which wrote ASHRAE Guideline 0-2005, "The Commisioning Process" expected the process be applied in this fashion.

I suppose one could have the CxA perform the functional testing, but there is a significant incentive lost if the installing contractor is not required to complete a successful testing cycle first. The incentive is simply that the installing contractor will want to only do the test once, and not be subjected to repeated callbacks because the installation is not working as the Engineer intended. If a third party is doing all of the testing without the contractor's involvement, there is no financial incentive for the contractor to make certain his installation works as intended. The retainage held on most projects is typically not enough to insure the contractor will return to correct problems. The Cx process applied with the oversight of a qualified commissioning provider limits errors in both design and construction by focusing the entire project team on delivering quality to the owner. That role does not exist in most project teams.