There have been many white papers about stopping at parallel and reversing directions when squating. Other research that say going any lower than parallel is a danger. A case can be said for both studies. Though when helping people with squating, I have them go a few inches below the parallel line. I believe that stopping at the parallel point (or just above) is something that should be avoided. Just my view, that's all. This goes for sets of 2's or 20 reps.
Olympic lifters come to mind. Doing 400-500 squat cleans, ass almost touching the platform, is very impressive. These are front squats (with heels raises for better balance), with focus more on the front quads, and the knees, than regular back squat. Front squats are very hard to recover from when in that extra deep position after the clean. But, for the most part, the knees seem to handle that extra stress well.
Let's face it, a lot of men just do not have the confidence to bottom out when doing regular squats. Or they were never taught the correct way to squat, which can give greater stress on the lower back. Back pain from squating can be caused by poor form/weight shift and balance. Combine this with too much weight on the bar (you might think you know how to squat...but maybe not as well as you believe ) can lead to trouble. Good Luck.