The original article did note that it was MFT and the DCT that were responsible for most of the issues. I
'd agree that the MFT stuff isn't exactly "reliability" in the sense of critical problems for long-term ownership -- but it certainly would be annoying if it didn't work. Since the scores are accumulations of past data, it's not clear how MFT software updates affect the ratings.
As for the DCT -- well, I bought a manual, in part to avoid those problems. That particular part isn't Ford's best job.