I read the Ingraham post, and found it a nice thought-provoking read. While he spends much time trying to debunk a strict Postural/Structural/Biomechanical (PSB) approach, he only glosses over a more systemic approach. He does make reference to "psychosocial factors" but not much beyond that.
I can tell you that our class was drilled relentlessly on the ICF Model, (International Classification of Functioning, Disability and Health), which better resolves Ingraham's grievances by including environmental and personal factors. Beyond that we spent some time learning about the nature of chronic pain (nociceptors upregulating resulting in increased sensitivity, decreased motion, and so on), which also seems to better account for the "squishy, messy physiology" that he seeks.
I can tell you that in my brief clinical exposure (I'm about to begin the meat of my internships) I've noticed some PTs downplay or pretty much ignore psychosocial factors that are likely at play in some patients. And even when dealing with patients themselves, some of them seem skeptical if you discuss some of these factors with them as contributing to their pain (e.g. how the recent stress of losing their job and apartment are related), and would prefer a black-and-white PSB explanation.