I assume you are primarily referring to the detrimental effects of a heavily loaded deep squat. I'll quote below from a response from a trainer I respect quite a bit as to whether it was ever appropriate to squat deeply and allow the knees to move forward of the ankles. I think there is a lot of wisdom here.

"That is an old myth, that knees are not supposed to go past the toes...okay well then answer me this: how are you going to pick something up off the floor, go to the bathroom, walk up stairs, etc., etc. without your knees going past your toes...you cannot. in fact, it is actually unhealthy to not squat fully or ass to grass. we have gotten so use to the 90 degree squat, 90 degree seated position in chairs and car seats, planes...it just tightens up our hips/back, even our ankles / knees and makes a full squat even harder. the 90 degree squat forces people to compensate as we must bend forward more from the hips and stress the back out even more. the 90 degree position never challenges our ankles either, so in the end we get less and less ankle ROM as well and this feeds into the same thing as the 90 degree seated or squat position, it lessens our healthy ROM and then forces us to adapt and bend in ways that are NOT healthy, the more we adapt, the greater risk of injury and pain. this is why we have so many back problems in this country today, half squatting, limited ROM in the hips, ankles, knees. when in doubt i always look to nature or what is natural and innate in all of us...so in our case, how do babies squat? they squat full ROM, ass to grass with their spine vertical. they do it 100% of the time, perfect form, then at some point we begin wearing shoes that conform our feet (less ROM in the foot), we begin to sit in chairs and seats at a 90 degree angle (tightens our hips and creates again, less ROM in the ankles, knees, hips, back) and we lose all the beautiful movement skills that we had as kids. my answer is to get back to full ROM, squat fully, go barefoot, let our bodies re-experience how wonderful and healthy we feel when we move fully and freely."

There is always going to be a "fitness competition" going on when it comes to what's best. One person does some research that proves one way to be better than another way. Then someone else comes along and their way is better. When I was younger I liked the idea of just following one person who I agreed with when it came to fitness. I would get really into their way of doing things and then as I became more educated my mind would start to tell me that this guy who is training me is very one dimensional. I might mention a theory someone else had and the trainer would get offended, and argue the fact that his method was better. That was a huge turn off. NOW I just train how I want to train. If new methods come along I try them. If they work then I keep them and if they don't then I leave them. I take bits and pieces from everywhere. Essentially I am a sifter, taking what benefits me and leaving what doesn't. I am 31 years old, I have been training for various things since the age of 5. Most notably was a 20 year stint with water polo. I had a great coach in high school with limited knowledge in the art of training an athlete but he read an obscene amount of literature and had us doing plyometrics and circuit training during the season and russian strength training in the off season. At the time I would call this cutting edge for a high school coach. That was almost 15 years ago. We were successful and we won a lot of games. In hind sight I can see our range of motion was suspect, we never stretched our muscles dynamically or statically and had a mixed result of semi explosive, strong bodies, with limited range of motion and power application.I guess my point is, there is always going to be research that supports and opposes everything. Instead of listening to everything other people tell you and being a sponge be a sifter. Take what works for you and leave what doesn't make you better. Currently I train my nervous system using Gavin's methods, I surf, paddle, swim, run, olympic lift, do gymnastics and yoga, and try to eat food that is not processed. I do my best without dying from stress related cancer. You should do the same.

Not sure if your comment was directed at me but I agree with you wholeheartedly.

"Instead of listening to everything other people tell you and being a sponge be a sifter. Take what works for you and leave what doesn't make you better."

I've been doing this for years. My comment was in response to the "It's never okay to squat deeply." implication in T's article. In my experience, there are few true absolutes. I have found that simply paying attention, listening to my body, and not worrying too much about any of it works best for me.