The shoulder can be the most difficult to treat. Multiple diagnoses can be made, depending on the Physios experience.
If there was no direct trauma and assuming no condition like Rheumatoid arthritis, Gout etc, then it is likely that the problem is refered pain from the spine. In general, Anterior shoulder pain is from the upper Cervical spine, lateral pain is from the C6,7, T1 area and posterior pain from the C6 to T3 area.
So, in your case the pain is under the Scapula, left more than right. My interpretation is that you have a problem at the level of T2 - 5. Originally you were probably not aware of the spinal problem because the upper Thoracic spine is quite rigid and doesn't move enough to cause local pain. But eventually the inflamation from the damaged ligaments radiated laterally, causing chronic muscle spasm in the Scapula area and now into the Sub Scapula muscles.

So the Physio may choose to mobilise and or manipulate the spine + or - the other Physio treatment modalities.