When we perform a back squat it is perfectly ok for the knees to pass over the toes (working the quads more in comparison to the gluets) ONLY if you have the flexibility to prevent the heels coming off the floor. ALL the force from the movement should be placed over the centre or the heels of the feet.
When you squat with your butt moving further back and knees not going over the toes, you will work the quads less and gluets more.
The reason why you hear this lot is because most people have poor flexibility in the ankle joints. Stretching may overcome this problem but not all the time. Working the antagonistic muscle groups will also help with flexibility of the agonists.
If you have below average calf flexibility then keep the knees back in your squats, which looks more like a deadlift.
I have been giving clients the knees over toes squat for a while now, not to mention myself for a few years and never had any complaints.