I am going by the word of my physiotherapist and a FMS certified specialist, and their testing which I saw with my eyes. It was evident that I had a significant difference only in my external rotation range of motion (my right side having much less). My internal rotation was fine. Also, I feel it myself that their is a large restriction on my right side doing external rotation work (this was even before going to my last physiotherapist). 

Another point is that limited external rotation would be more logical in terms of why it may be contributing to the patellofemoral pain: Limited external range of motion on right side–>limited glute activation on right side–>tight IT band and/or knee valgus–>lateral pull on knee–>knee pain 

For my case the knee valgus isn’t as a big of an issue  at least based on: 3-D gait analysis, and physiotherapist examination, and FMS examination. None of which could find any significant knee valgus or differences between both of my legs

I dont see how limited internal range of motion would be related to knee pain. Maybe something I can bring up with my physiotherapist.