Well as far as I'm concerned, when I low bar squat I can maintain a more vertical shin angle (it still travels forward, but not as much as in a high bar squat) and the knee suffers less. That's why I can squat low bar and I can't high bar. When I squat high bar that thing that moves in my knee, in the lateral "hole" of my right knee, when I get to about 20 degrees of flexion, starts to do some damage. Damage that can be avoided by squatting low bar.
It might be that my hip (and not only hip) flexibility sucks so bad that I really really load the knee and the quads when I high bar squat. For example, I couldn't even do a empty barbell overhead squat IN OLYMPIC LIFTING SHOES today. Granted, with a pretty narrow stance but still. I was able to do them with good form using a 10 kg bar though.
Not to mention front squats... with an empty barbell and o-lifting shoes on, the bar doesn't even touch my chest, let alone sit on the shoulders. It sits entirely in the hands, with elbows pointed down. There's no way to make it sit on the chest (don't even mention a proper rack position) unless I increase the weight so the weight of the bar presses on my hands more. Otherwise... no chance, no matter what grip I choose.
So there are a ton of inflexbilities there.