I have never heard such a thing about back squats and I think it would largely depend on your form. If you have a medium stance and you spread your knees out, then it you would most definitely have your toes being crossed by your knees. If you use a wide stance then that would be very hard to do. If you mimic a powerlifting squat where you try to "sit back" with a medium stance your knees will not cross your toes by much - if they do which I think they probably won't. If you try to squat "down" like an olympic lifter or a regular weightlifter (no need to label anything here because that causes a huge commotion) you will not be able to use a very wide stand and it will be hard for your knees not to cross your toes. If you squat to a box then again it would depend on the width of your stance. Confusing, right? Thats why I said the knees over toes thing is BS and it really depends on the lifter and his preference.
Front Squats are better than back squats because they:
(a) Hit your core a lot harder
(b) Require technique
(c) Have a better carry over onto your other lifts
(d) Are better for athletes