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Those are good points. I don't have time to devote fully to the question right now but in addition to the above-mentioned points, the short answer is that I've found that deep squats are really helpful for acceleration (when joint angles are very similar). Also, posterior chain recruitment is highly linked with squat depth so if you agree that posterior chain strength is important (as you should) 1/4 and half squats do not hit this very important muscle action to the same extent as deep squats.
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