I am not sure of a way to tell in the actual throwing motion. I am just a dad and know very little about this.
The PT showed his lack of IR by comparing his IR via the Sleeper Stretch on both sides. His throwing side would not rotate without his shoulder blade moving forward with it.
He had done normal stuff (only 14) not heavy lifting. Pushups and light weights etc..
Unfortunately if your scapular muscles are not activating then instead of these exercises making them stronger your body finds a way to adapt and do the work with the wrong muscles. This puts undo stress on rotator cuff, labrum etc.. etc....
I feel they are neglected because he has gone to pitching guys and workout guys etc.. and they have never mentioned it. They normally talk Rotator Cuff and elbow.