I'm sure there are many, but I'm not aware of any deep study as to the affect of raised heels for BB'ing squats and the damage they may, or may not, do to the structure of the knees.
I am aware of the biomechanical analysis of front squats (with Olympic lifting shoes) that there is less stress on the knee region than with flat footed squats. And overall easier on the knee's. Poloquin (top strength coach) has, among others, presented this in some articles on different forms of squatting. Raised heels (either with front squats or regular squats) require the quads to work harder, not the knees. Also the importane of a strong and balance hamstrings to assist in any form of squatting. The heel drive will also become more pronounced with raised heels and will produce less stress on the lower back.
If you have a potential knee problem, bad knee or a sense of injury happening,than don't raise the heels (I most always tend to heavy squat barefooted, which give a better feel for the exercise and helps surfing very well). Just that some guy's have trouble with balance and leaning too far forward when squatting. And again, the lower back problems with this exercise for some.
The mean average of a man is between 22 to 24 before the cartilage between the rib bones loses it's plactic state and becomes harden. If you are younger than that average, the chances greatly increase that the rib box will expand to a larger size. Through the 20 rep squat and the extreme breathing that it demands. The proof is that perhaps thousand of men have increase ther chest size from 2 to 3 inches, over the years, with this type of progam. One only has to experience such training to understand the results obtained. If you have a chest size of 44 (guessing that would be the average for a GB'er) than wouldn't a 46 to 47 chest size be that more impressive? After a set of killer 20 squats, a light straight arm pullover is performed. Main purpose, for the stretch to the rib box/chest. Good Luck.
Side bar: The Olympic lifting shoe is raise about 1" or an little more, depending on who ever makes it (and the socks or pads one may add). A 2" board (2X4) is actually 1 & 5/8's to 1 & 3/4's, given the age and condition of the wood. A few cross training shoes have a raised heel.