You're looking at this incorrectly. The squat is a movement and should be trained as such. The difference between training a muscle and training a movement is the technical aspect and analyzing weaknesses within the kinetic to strengthen the movement. 5/3/1 is about becoming stronger at the four core movements: squat, deadlift, bench, and overhead press. The assistance lifts are there to strengthen the weaknesses in the movement. It is incorrect to look at these main lifts as training a specific muscle and doing so will limit your progression.