Yes it looks like you are just hitting parallel.
But remember: the Low Bar Squat, as described in SS 3rd edition, is performed to just below parallel.
You were probably experiencing knee pain because either you were bouncing off of your knees instead of your hips in the bottom and/or your knees were sliding forward in the bottom of the squat.
In the video you posted your knees are sliding forward in the bottom. Your knees should track in line with your toes during the first half of the descent and then be set in the position they will stay in for the bottom of the squat. They should not shoot forward as you break parallel. This represents inefficient mechanics and can lead to knee pain. I recommend working with a TUBOW to dial in your knee position: How to use the TUBOW