Dude, I do yoga three times a week. I go this deep with a kettlebell and probably front squat too. I think it's mostly fear that I don't with the bar on my shoulders.
It's an anterior core issue. The kettlebell and front squats fire up your anterior core, hence you're able to go deep. With a back squat this doesn't happen so your movement is restricted. Work on planks and hollow holds (don't brace your abs too hard, let your body do its thing, they are anti-extension movements so don't crunch up or you have no benefit doing them).