The theory goes that calf muscle (I expect the gastroc since it’s higher up and biaxial) and hamstring muscle bunches behind the knee and that compression becomes the axis.

But the problem I have with this is… why would it bunch up there?

The hamstrings are busy assisting the glute as spinal erectors or being a dynamic stabilizer. The gastroc is helping the soleus work as a plantar flexor.

Would they just hang around there?

Even body fat… if the knee becomes the highest point on the body, why would the fat climb up to the that point to hinge behind it? Fat inferior to the knee should be pooling towards the ankle. Fat superior to the knee should be pooling towards the glute!

http://www.marksdailyapple.com/squat-poop/

If you do the squat to parallel or do the eccentric part of the squat too fast then less muscle is activated and the stress of the movement is concentrated in and around the knee. The quads, cartilage and ligaments all bear the brunt of the weight whereas the glutes and hamstrings bear little.

The deep squat is beneficial because below parallel the glutes and hamstrings are fully activated in the concentric and eccentric phases.

Forming the biggest muscles in the body the glutes and hamstrings play a crucial role in protecting the knees by absorbing shock/stresses that would otherwise cause wear and tear of the knee.

There are two camps out there one that says deep squatting is good for you and one that says it is not. In both camps there are medical professionals with a lorry load of qualifications. I don’t have a medical qualification to back up my understanding of the benefits of the deep squat so I reserve the right to be completely and utterly wrong. LOL!