ROH:
Of course all of that is in the index. And the index isn't a "theory"; it is putting a wide range of realities into a number for statistical purposes.
All of those issues you raise can and do happen in schools even at the top of the index, but the higher the PI number, the more common those realities are.
Part of success in low poverty schools (whether athletic or academic) is highly correlated with the low amount of negative impact that real-world poverty has on the children who provide the data upon which we make these judgments.
When I taught at Woodruff (for 18 years), it was more common than not that students at the high school did not seek medical help for much of anything. That was cultural and financial. In sports, it was a nightmare. Injuries were just tolerated and players, because that was how they lived their lives, were content just to let injuries run their course.
The PI is highly correlated with many aspects of the cultures of schools. For soccer, affluent schools tend to have families that see club and/or year-round soccer as the norm—because they can afford that for their children. Thus, success on the high school pitch.