I treat each player as an individual, if they have the flexibility to squat deep, then that is what they do. If they have any pre-existing conditions that prevent from doing this then we squat higher. I aim to try and get the majority of players squatting just below parallel, however, I also have players that do not squat at all and they can still perform well at the weekend. A good measure of depth is to see if you could hold a pencil in between their thigh and calf when in the bottom position of the lift, if they cant its probably too high.
Also in my opinion everything done in the weight room is general preparation. Specific preparation is done through rugby training and of course the game itself.