Their methodology is inherently flawed. From a quantitative standpoint, they leave out strength of schedule, weather, etc.
From a qualitative standpoint, they don't address this at all. Leadership and motivational qualities, how they treat players, etc.
This is the problem with PFF. They try to break everything down into quantitative items, and certain things absolutely cannot be measured that way. But hey, they try. The PFF results are absolute crap much of the time for this reason.