I agree with this in theory. The reality I see in commercial gyms makes me think that most people would be best served by going at least to parallel if not hip-below-knee.
The reason I say that is because it's just a fact that shallow squats are easier, and what happens is people with lousy form end up putting way too much weight on the bar when they squat shallow. You don't have to be squatting ATG to hurt your back, in fact from what I've seen most of the people with the worst form are squatting shallow. I see lots of guys rounding their backs on 1/4- or 1/2 squats because they've got far more weight on the bar than their trunk/core can properly support even through a limited ROM.
Another downside of shallow squats is that it's likely to create or exacerbate muscle imbalances since the outer quads are doing the majority of the work. The inner thighs don't really contribute much unless you squat deeper. Not to mention the lack of posterior chain recruitment.
Agreed on all points. My "default" choice would be hip-below-knee. But other (reasonable - 1/4 squats don't count) depths will work almost as well. I find some people just get too dogmatic about squat depth.