I've spent 20 years in the gym environment, and the educational training I did for my work pre-dated much of what is now considered 'functional training'. Yet I somehow think we're missing some connection between what exercises are done, associated joint and back pain and the loop back to a better way of doing exercise.
Universally the instruction for squatting is to go no lower that 90 degrees at the knee, yet if I asked you to lift a heavy object, instinctively you wouldn't bend that much to lift.
Most people I know when bending to that angle causes the low back to start to flatten and this puts it at greater risk of injury.
And for many with knee problems, an underlying issue is muscle imbalance in the quads, where the medial part that works most in the last 30 degrees of leg straightening is weak relative to the outer part of the quad. So doing deep, heavy movements by default creates an imbalance, which is often then exacerbated with leg extension type exercises.
My theory is this:
1. Any squat type movements should only be to 45 degrees at the knee when loaded with weight. So this includes squats obviously, leg press & Hack Squat.
2. Full depth movements such as lunges should be encouraged so long as the back is well stabilised with the core muscles. These can be weighted to help build bulk for those wanting it.
3. Full depth squats (bum to the ground and heels on the floor) is a practical means of maintaining full range of movement, function leg strength, and since it should be done without weight reduces the risk of back or knee injury.
Restoring our capability to live to the boundaries of how our body functions makes more sense than doing an exercise purely because we can. This is what functional training is really about.