fwiw, olympic style weightlifters have been lifting and squatting with elevated knees for decades. no problemo with knees.
i have squatted in three main styles -
wide stance, flat soled (converse all stars), bar low on back to just below parallel for powerlifting
narrower stance, elevated heels (adidas wling shoes), ass to ground - for weightlifting training
and
narrower stance, elevated heels (ditto), to just below parallel - for hypertrophy
they all have +'s and -'s. obviously, if you are training event specific, then a certain kind of squat will be preferable
if you are going strictly hypertrophy, i think there is good reason to adjust your height on occasion
above parallel (1/4 squats) are good to overload the quads and get your nervous system used to higher loads on your back. (same as walkouts do)
these aren't "cheating" if you are using them for a purpose.
i haven't done a competition in a while, but i still squat generally OLer style because i most prefer it and i think it gives the overall best benefit.
atg isn't so much the problems with the knees, it is bouncing out of the bottom (pushes the patella forward at the lowest point). bouncing is GOOD technique for a wler (as is bowing on the way up), but like almost ANY athletic endeavor, you sacrifice safety for sports performance
if one is lifting for pure ego (to do as much weight as possible), then a PLer stance (wide/low bar) will enable most people to do the most weight. but it is not very quad intensive
all depends on goals
for most people interested in hypertrophy, i would recommend high bar, not all the way to ass to grass (so called bber or athlete's squat)
and on the sports thing, I know one OLD ol'er who only squats about a 1/2 squat at best (actually a little above parallel). it's not cheating, because that's the depth he takes his clean and jerk as well. so it makes sense
as usual, goals defines means