I read this article and, somehow, it struck a chord in me. It seems to make intuitive sense to me. how do the rest of you feel?
http://themovementfix.com/the-best-kept-secret-why-people-have-to-squat-differently/
While it's true that there's anatomic variation, not all of these differences will change the way you squat. Femoral anteversion or retroversion will definitely affect how much you toe out in a squat. However, that doesn't mean your knees should fall inward at all. Same thing with a tibial torsion. Coxa vara and valga (shorter or longer neck of the femur) will change your muscle efficiency during different parts of the squat, which may be a portion of why some people can push out of the bottom without a problem while others have significant difficulty.
In addition to all these things, anthropometrics play a big role as well. Your torso to lower extremity ratio. Your femur to tibia length. In addition, ROM is a huge part of squatting. In reality, range of motion (ROM) limitations are the biggest thing that cause excessively varied squat form. So don't use the article as an excuse to squat poorly. If you do have to toe out a little bit more, then fine, but then again you don't know your anatomic variation. You could just be doing that because you have lazy glutes (glute amnesia, poor glute activation).