Knee pain in squatting can be caused by any number of things:
- Poor technique
- Tight hips
- Tight IT bands
- Foot angle
I agree that box squats should be done slightly above parallel especially to begin with but that is to be coupled with a wider than usual stance and an upright shin angle to overload hips, glutes and hams not just to enable you to squat high.
Haven't read the article but the above excerpts indicate a clueless author with too much time spent in books and not enough time spent in the gym.
Don't call it a comeback