Anthony McCord is new MTA Chief Transformation Officer, and everything this remains (intentionally) confusing. He's announced by the MTA but is subject to an MTA Board vote and reports to the Board (rather than to internal MTA management).

http://www.mta.info/press-release/mta-headquarters/mta-selects-anthony-mccord-chief-transformation-officer
Additionally, the Alix Partners report is such a flimsy document that the MTA, at Cuomo's behest, is just running with, and it includes significant investment at the C-suite level at a time the MTA is supposed to cut costs. Most of these roles are duplicative.
This whole thing would make a great business school case study in how not to transform a bureaucracy, and yet, it's the path New York's giant transit system is careening down. Kinda boring, very important.
It's also still quite reasonable to think this is either an end-run around the legislature to quasi-privatize or laying the foundation to privatize the MTA. Where's the Assembly/Senate hearing here?
To me, the overarching question surrounding transformation is "what does Andrew Cuomo want out of this?" I don't have a good or any sense of the answer yet.
Here's @danarubinstein's story on McCord, to which I say to the highlighted part "lol yeah right."

https://politi.co/2O7liLf 
I bet McCord's past experiences, per his LinkedIn profile, will go over well. Look at this focus on eliminating jobs and closing unionized production sites here. @ReinventAlbany calls him a "hatchet man."
He gettin' paid. https://twitter.com/danarubinstein/status/1194688157444431872
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