I am going to take a guess at this and I reserve the right to change my mind since I have not thought this through very much. When people's knees track medially, or valgus, to use the parlance of our times, during the squat, they are shortening the adductors. The adductors function largely as hip extensors during the squat, provided the knees stay out. Letting them come in tends to flex the knees slightly, shifting work to the quads, while removing some of the contributions of the hip extensors. Knees coming in also often occurs in conjunction with lifting the chest. So, knees coming in probably allows for a slightly more upright posture as the knees rebend and takes some moment force off of the torso. It also potentially slows the bar speed, deprives the spinal erectors and hip extensors of some work in favor of the quads, and puts a twisting force on the knee. It is a function of standing up "by any means necessary," instead of using the musculature in concert to drive the bar up. That's my first crack at this.