Interesting read. Good to see a variety of opinions from kinesiology/physiology professionals. I tend to agree with the opinion that the squat should generally descend to the point of lumbar-flexion and butt-wink. I do, however, disagree with most that I think the partial-squat can have a place in sport-specific training if programmed in right. Its analogous to doing rack pulls as part of a DL progression IMO.
Miaou's right in that it's not a very good analogy.
But it works in that both are something to be approached judiciously. With rack pulls, someone has to consider first, are they having trouble at that point because of technical issues that arise earlier in the lift? And is this something that could be better trained with bands or chains? And if partial pulls are being used, actually using a reasonable ROM, weight that allows actual work to be done, and isn't just about loading up the bar, and making sure that the higher starting point doesn't change that part of the lift.
Perhaps you can tell I don't think rack-pulls should be a staple exercise for a great may people?
Similarly, there are certain cases where partial squats might be beneficial for someone participating in a specific sport. If they are used, it'd be after a considerable amount of work developing a strength base, including plenty of full squatting. And as training progressed, some squats, depending on where in the training cycle someone was, could be partial squats. And it wouldn't be an excuse to overload the movement, but almost certainly be explosive work done with lighter weights.
And that's if there aren't even more specific exercises to fill the sports specific role of partial squats. In which case all squats would be full, and done for developing GPP/strength base. Also considering that something that might appear to be like a partial squat, say, jumping, may be a fairly different movement - partial squats put more emphasis on the quads, where as jumping, and many other "athletic" movements are powered more by the glutes and hamstrings. So even if the ROM seems similar, it doesn't mean the muscle involvement is.