Well to be honest i would never squat on a SM. It's so un natural IMO. You end up basically leaning on the bar to help balance and keep you upright.
Many people go off free weight squats because of back/knee pain. Main reason people get these problems is because they don't know how to squat properly in the first place. So many people who squat get lower back pain from their lower back rounding, but there are ways to solve this etc. Knee pain can be due to lack of ankle mobility, and such people who squat 'using their knees' rather than focusing on raising the hips.
I'm not saying SM and all machine don't have their place (as they obviously do) but i'm one of those who RARELY use any machine and believe in free weights and working those stabilisers to the max