Basically like the others said for full squats the bar is higher and for parallel or whatever the bar is lower. I think exact bar postioning is up to the individual but whatever position the bar is in the biggest thing that will be affected is torso angle. A higher up bar will mean a more erect torso and a lower bar will mean more forward torso angle. Your body in a properly performed squat (one without big deficiencies) will tend to keep the bar over the middle portion of the foot...thus the changes in body angle. Biomechanically this just needs to happen because of the center of mass. If you want to see this effect do a front squat with a good bit of weight (for you). The torso angle will be more erect than either high or low bar back squats. Even though the bar is very high the center of mass is more in front of you so in order for the bar to be kept over the center of your feet the torso remains more upright.

If you look at the bb.com article you see rules about 45 degree angles and such. Such things are biomechanical nonsense. The center of mass will determine the torso angle. Trying to force you body into a postion that causes this cener of mass to be offset will result in a failed or a slowed lift until the weight can be brought back into the proper position. Proper form is as much a matter of body learning and the maintenance of movement patterns as it is an adherence to "rules".

You can see the effect of the "rules" vs. body by using a weight that is too light to learn how to squat and deadlift for instance. Now a lot of us will say you need to start with a light weight to learn but of course it needs to be heavy enough to actually require proper form to be lifted correctly. If the weight is too light you can basically lift it with a form that would not achieve success at a heavier weight. Of course a too heavy weight would mean not being able to overcome the weight in a biomechanically sound way and so similar problems (with perhaps more dire results).

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If you act sanctimonious I will just list out your logical fallacies until you get pissed off and spew blasphemous remarks.