I'm working with a physical therapist to help with my snapping scapula. She's having me do these funky push-ups where I have to hunch my shoulders forward at the end of each one. How does an exercise like this help people with problems from snapping scapula?

The exercise you've described is a standard push-up with a plus. The "plus" is the part where you hunch your shoulders forward. This part of the exercise is designed to strengthen the serratus anterior muscle, which attaches to the edge of the scapula nearest the spine. This muscle passes in front of the scapula, wraps around the chest wall, and connects to the ribs on the front part of the chest. Working this important muscle helps align the shoulder blade and can add some extra cushion between the shoulder blade and the rib cage.