I agree that the blame lies almost entirely with the supervisor who sets such a narrow reading list, researchers who do uncontrolled studies, and publishers who publish them and publish articles like this one.
The thing that saddens and worries me, for the PhD student, is the apparent lack of curiosity.
I am trying to imagine myself in such a position, and hoping I would have explored more widely. Even just googling the conditions specifically mentioned - CFS, FM and IBS would have raised loads of issues that a good researcher should explore - biomedical research, patient support groups and what they say, etc.
What has happened to scientific curiosity? And integrity?
But then of course, the student may have done this, and been told firmly to stick to the supervisor's orthodoxy if they want to get their PhD and get papers published, such is the narrow world some academics live in.