That about wraps it up. But let me play devil's advocate here for a minute, if nothing than for the sake of discussion.
Strength is obviously the primary concern for members of this board, and that's why we squat. A lot. Some trainees, however, have other goals than just strength where the squat is still a useful tool, such as in developing a pleasing set of glutes. I've seen the paper below used as an argument for squatting ATG instead of just breaking parallell, especially if your goals are more based on aesthetics than strength. The primary reason being that ATG squats activates the glutes more than in a parallell squat. Here's a paste of the relevant portions with some added emphasis:
Source: The Biomechanics of Squat Depth - Brad Schoenfeld
So there you have it.
I find it curious that the paper deals with muscle activation and focusing on glutes VS quads, but nothing about strength as a whole. I wouldn't know what to argue here if a trainees goal is Dat Ass and uses this paper as evidence to do ATG squats. If their spine lumbar doesn't go into flexion when they squat ATG then have at it for all I care. Hell, they can do it if their spine is all over the place. I'll keep squatting to slightly below parallell and mind my own business.