Personally, I set the safety bars to about 2" below parallel. Except for once when I lost balance forwards (that was exciting!), every time I've missed a squat rep it's been coming out of the hole ... and it's been easy to just set it down while maintaining correct back posture.
I think that squatting as far below parallel as you describe you're probably leaving some strength gains on the table unnecessarily - which is why Rip's recommended breaking parallel, but not going ATG. I also think that you may easily also be making it somewhat less safe to put the bar down in a failed rep, if you have to risk dropping your chest to set it down.