When in the amortization phase, or hole, different musles are going to be stretched/strained depending on a few things. These factors include whether you’re using your bodyweight alone, or if you’re doing a weighted front or back squat. In addition, your stance may change things as well. I find if I’m in the hole with a wider stance, I’m naturally going to experience a stretch in my groin.
As far as it stretching your hamstrings or lower back, it’s hard to say. Once you go below parallel, it’s said that the majority of the strain comes off the knees and lies on the hamstrings, so that’s what you might be experiencing.
Regardless, it seems to me that you enjoy going balls deep when squatting so I’d suggest to continue going with the high bar squats if it’s doing such wonders for your hips.
All the best,