@duncan
Elsewhere, I've stated a couple of other aspects of the debate which don't fit usual dichotomies. One is that a persistent pathogen
is an immune dysfunction. Healthy immune systems are remarkably good at either destroying pathogens, or forcing them to remain inactive. We now know things that Koch did not know about such standbys as
mycobacterium tuberculosis. Most infected people do not show classic clinical signs of TB. Even up to 99% of those who ultimately develop the full disease do not move directly to acute disease. There is a long period when most patient immune systems control it. Just a slight improvement in very specific immune activity here would make them effectively immune to the disease. In this regard the BCG vaccine, while useful, has proved a disappointment. Why don't we have a TB vaccine with high effectiveness?
Another modern problem comes from the Balkanization of medicine into specializations. Before a patient reaches a specialist dealing with Lyme or ME/CFS she/he is likely to have consulted several doctors. If any of those recognize a serious problem connected with a single organ system, like the heart, pancreas or kidneys mentioned above, the patient will be shunted into a different therapeutic track, and the doctors for less-specific diseases will never see them. It doesn't matter that many recognized conditions are "of unknown etiology", most specialists aren't concerned about anything except severe disease meeting their diagnostic standards. Part of the reason is that available interventions may be as drastic and risky as a heart bypass.
The result is that statistics associated with neglected diseases suffer from serious sampling errors because various doctors in high-prestige specializations like cardiology "know" the problems they treat have nothing to do with less serious preclinical conditions. Not only do patients who somehow avoid going down the path to immediately dangerous pathology suffer neglect, those patients who do were not given any useful advice which might have prevented disease except exhortations to eat healthy, exercise and avoid X, Y or Z.
After some effort in searching literature on the effects of exercise I have concluded that nobody had carefully tested to see if causation was always from exercise => health instead heath => exercise. If they had, the discovery that a few patients have reduced capacity lasting long after exercise would not have been a surprise.
I have also noted that people who have great trouble "eating healthy" usually pick foods with high energy content to splurge on. In one case, the patient was not able to control weight despite really drastic measures. Last I heard, her pituitary was almost completely calcified. This not only raises questions about incidence of pituitary damage for unknown reasons, it also makes me wonder how much of "healthy eating" is a lack of craving for unhealthy foods caused by metabolic defects. Had diabetes been labeled "chronic thirst disease", and considered subjective, I doubt research on it would have gotten very far.