Read the overview and he explains why he chose the box squat. The biggest reason is probably a practical one. EC is not a guy who has ever really believed in writing cookie cutters but he sort of felt compelled to do one (maybe to right some wrongs
).
The program is pretty ball-busting and box squat are 1. going to produce a corresponding increase in free squats expecially since free squats will be practiced DE style and you have the option of technique days. 2. this program assumes that you are not a beginner but you are sort of new to this kind of advanced strength training..as he says, this is kicking it up a notch for most. Box squats are a good choice becasue they guarantee that the depth at the beginning and end are the same, same technique, etc...it's simply nice and consistent compared to what would happen to many on free squats. You are kinda preoccupied with depth anyway when you should be more occupied with quality. It's better to do, imo, 10 just below parallel box squats with proper form than it is to do a couple of free squats that are too deep and the back rounds out, etc...
Well...this is why I would have chosen the box squat...I don't want to speak for him but it would simply be a way to maintain quality and consistency since he won't be there to supervize.
I'll be happy to ask him for more of an explanation. Or you can of course.