Let’s start with why this cue came about in fitness professionals. It is true that when your knees go over your toes, there is an increased force in the knees. However there is an even greater force on the hips when there is a resistance to keep the knees from going over the toes. In addition, if you are squatting below parallel then your knees have to go past your toes. If they do not then you would not be able to maintain an upright torso.
It all comes down to where the movement is initiated and where force is generated from. If you are leading your squat by bending at the knees and letting them come forward, then there will be increased force at the knees. However if the squat is initiated by breaking at the hips first then there will be less force at the knees and decreased risk for injury.
In addition, if you are trying to squat below parallel you have to let your knees go past your toes to avoid compensation in other areas of the body and keep an upright torso. If you keep your knees from going past your toes in a deep squat you will have bend at the waist putting your back at risk for injury. You can see in the diagram below that to maintain proper form in a deep squat the knees go past the toes to maintain the upright torso position required.