The other variables to consider outside of form can largely be influenced by Assessing, Programming, and Progression.
I agree that good form doesn't just give you a pass to do the exercise a million times per week with as much weight as possible for as many years as possible. I think the sport analogy was a good one in that respect. Lifting heavy things needs to first be progressed properly but also programmed properly. Also, assessing will give us a lot of information in relation to whether someone should or shouldn't do a certain exercise or load a certain exercise (this will tell you, for example, if someone does suffer from sciatica, in which case heavy squats may not be the best option for them). Stones will still be left unturned, i'm sure, but it's not a complete guessing game and there are a lot of really smart people out there developing ways to take the guess work out of the equation. It's came a long way and continues to develop at quite a fast rate.
Overuse isn't sudden, either. It creeps up. Common sense will recognise the signs before it's a serious issue but, as "they" say, common sense isn't very common, and i'm a good example of that myself.
I had a rant on "function" or "functional" in another recent thread so I won't go into that much. In short, our "function" is really the movement (and stability) patterns that are hard wired into our brain and develop as we develop from baby -> adult. It's instinctive and not taught. This includes squatting. Now, i'll be the first to point out that this does NOT include squatting with a heavy bar on your back just squatting as a "movement". However, I do believe you can define "functional", and this doesn't mean everything you do should be functional, it just means you should be able to move like you're supposed to before you go add heavy loads to those movements. If you can already move well then you don't need to worry about being "functional", you can do whatever wil;l get you towards your goals. If you can't move well, though, it should be a concern and a priority and therefore what you do in the gym would ideally be "functional". This is atleast how I see it.
If you're NOT "functional" i.e. you don't move well, then certain exercises will help you, and certain exercises will hurt you. If your squat pattern sucks, for example, a leg press will only add to this in most cases, where a free standing squat performed "correctly" may help (it really depends on why the squat pattern sucks).
There are even exceptions to this. I have a client who had a stroke at birth and therefore a loss of function down one side compared to the other. One of his legs (the one with less function) is at least 6 inches shorter than the other, too. I can honestly say i'll never have him do a BB squat
I've trained a handful of people with true sciatica, have one right now with some of the worse sciatica i've dealt with. No, she doesn't squat. I didn't even need an assessment, just a "history" or actually, just a conversation. I've trained loads of people with back problems, some have eventually BB squatted and for some it's never and probably will never become an option.
Really what i'm saying is, "it depends". In the same way that it's silly to say everyone should BB squat, it's going from one extreme to another to say everyone who does the BB squat will get hurt, even if performed correctly.