Originally Posted by Robert Callahan
The reason people typically get lower (though not always) in a high bar back squat is not because they have more flexible hamstrings, but rather because as I said above the hamstring is shortened by the anatomy of the movement. By shortening the hamstring you remove some of the tension and make it easier to get low without losing your pelvic tilt. This shortening also means that the hamstrings can no longer contribute as strong of a contraction though. So in order to get enough force production to get out of the whole the quads and hip flexors must work much harder.
If anything low bar back squats take much more hamstring flexibility to preform because of the extra tension put on the hamstrings when at full depth.
I'm not an expert on hamstring anatomy, but when you're at the bottom of the full squat, something's pulling on your lower back. It's either the glutes or the hamstrings, or both.
And you said:
"So in order to get enough force production to get out of the whole the quads and hip flexors must work much harder. "
I believe the glutes are what really help you out of the bottom of the squat because the hamstrings are shortened. I don't think anything you said contradicts what I said about the hip flexors though.