The reason why a distance runner has trouble getting to proper depth is because their ankle joint is shit and has no range of motion because their calves are tight and filled with micro-tears. Foam roll and start doing proper squats and your ankle ROM will improve.
The goal of strength training isn't just increased strength/power or muscle recruitment...it is also increased functional ROM and increased connective tissue strength as well as bone strength. By not going to proper depth you miss out on 1. some development of connective tissue strength and 2. proper development of glute strength (since glutes are activated more the deep your go as you begin your concentric lift in a more hip-flexed position).
The placement of the knee in relation to the toe has no bearing on the incidence of knee injury PROVIDED the other joints are in their proper place. Try walking up and down stairs without placing the knee past the toe. We walk around all day and perform daily activities all the time with the knee passing the toe.
The placement of the knee in relation to the toe during lunges and squats has more to do with the length of the limb segments than anything else. A short person may be able to get to full depth on a squat without even getting close to "knee pass toe".
The "don't ever put the knee pass the toe" is a myth. Now, IF your heels are coming up on a squat (or even if your weight is shifted to the toes instead of midfood/heel) OR your knees are moving inward ("push/force" your feet outward to keep your knees from coming in) OR if your torso is leaning forward on a lunge OR your knee is again moving side to side on the lunge, that changes everything and your knee will be at risk.
IF you can lunge or squat with knee pass toe without pain then there is no problem.
Now, I can point too many strength & conditioning specialist, PhDs, etc who agree with what I've written above, but I'm lazy and don't feel like doing the homework, so I'll leave you this with:
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Fry AC, Smith JC, Schilling BK. Effect of knee position on hip and knee torques during the barbell squat. J Strength Cond Res. 2003 Nov;17(4):629-33.
The above study examined joint kinetics during back squats under two conditions. The first condition placed a board in front of the participants’ shins, which restricted forward displacement of the knee. In the second condition, movement wasn’t restricted at all. They squatted normally and the knees were allowed to pass the toes (GASP).
Squat Joint Kinetics
The researchers found that restricting the forward excursion of the knees during the squat (not allowing the knees to go over toes) increased anterior lean of the trunk and promoted an increased “internal angle at the knees and ankles.”
The results showed a 22% decrease in knee torque and a 1070% increase in hip torque! That stress has to go somewhere. Keeping the knees behind the toes definitely reduces the forces on the knee, but those forces were transferred more than tenfold to the hips and lower back. Translation: that’s an ouchie.
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Alan