disagree slightly with t0ddday. squats are GPP. i don't see why doing them in one kind of shoe or another would have more carryover to athletic movements. i can't squat deep without squatting shoes but if squats are just a part, rep- and effort-wise, of my training then what's the problem? i dunno, seems like the kind of false-carryover thinking that maxent would go for.
also not sure where he's getting the evidence for squat shoes causing tendinopathy.
I agree that squats are GPP strength work. That's why my recommendation was to do ADE work (pistols, shrimps, dorsiflexion mobility, etc) in bare feet and do your heavy squats in whatever shoes you like. However...
I'm not arguing that squatting heavy in one shoe vs the another has more carryover to athletic movement but what I am reminding you of is that a lot of self trained athletes do neglect their mobility work, their flexibility, prehab, etc... And while it's not a substitute for it - the warmup and squatting in barefeet or flat soles is better than nothing...
For example, I remember seeing the lifters at Broz gym warmup... It was amazing. Barefoot broomstick work. These guys could sit in a deep squat and move the bar to front rack, over head, back rack, all while walking in a deep squat, shifting weight to one foot, moving hips back and forth with tremendous range of motion. This was their squat warmup and it didn't involve lifting shoes because it was designed as a hip opener and ankle mobility exercise... After this the lifters put on shoes and worked up to heavy triples of 2x body weight followed by a ridiculous amount of heavy doubles and singles...
My point is that if we take a weekend warrior and he isn't conscious of this - and he puts his oly shoes on before he gets to the gym and does all his workout in them he is going to be reducing his ankle and hip mobility over time...
This leads to my point about Achilles tendinitis. Again, sure if we are a disciplined athlete we are doing our Achilles and calf prehab and we don't need to rely on squats and squat warmup for this... But is this really true for everyone?
As far as evidence about oly shoes and Achilles problems. I'm not sure of any scientific evidence. But there is a wealth of evidence about women wearing heeled shoes and Achilles problems. Especially women who wear high heels for everything but jogging...
Given that evidence I don't think it's a stretch to believe that the anecdotal evidence I have is worth following...
Imagine you work a desk job and sit all day. Your main exercise is at the gym where you do cross fit or something that involves squats and for it you put on your oly shoes... This is your main exercise. Then you also try to add in running of some type. I wouldn't be surprised if you are more likely to suffer Achilles problems in this case than if you did your gym work without oly shoes.... If your job is sendentary and your main training is at the gym then you basically have your Achilles moving between inactive sitting and very shortened with your heel raise...
Now you throw on spikes and sprint? Or go run on the beach? Not wise. I mean look at the poster alestor who wears elavator shoes to make himself taller and has Achilles problems... Raising your heel shortens your tendon... That's a fact. I'm not saying it's dangerous to do once. Or dangerous to do it while squatting... But if your not aware of it and don't do anything to give it length it could be dangerous...