OK, I have the greatest respect for Dan Millen. However, for him to say that he doesn't know why Ford set it up that way is puzzling. I cannot speak for the its use in the F150. However, I will comment on it in the Mustang.
First of all, in the Mustang, it only skips 2nd and 4th at part throttle in regular drive mode. Under heavier throttle applications, it does not skip gears. It also does not skip gears in "sport" mode. I am not sure why anyone would want it shuffling through all the gears when just driving around town or in stop/go traffic. The gears are so closely spaced that using them all at part throttle is unnecessary. Having fewer shifts just makes for a smoother and more refined driving experience and likely saves some fuel as well. However, when you need quick acceleration, all gears are there and it keeps the engine in the best RPM range. With the Mustang, there are other drive modes that alter transmission behavior from Lexus smooth to drag strip firm and fast. It is actually a brilliantly thought out transmission.
I applaud Livernois for what they do. Maybe some people will like this. Thankfully, it is an option because I will be getting a flex fuel Livernois tune for my Mustang and if it eliminated the skip-shift feature under light acceleration, I wouldn't do it.