It wasn't that long ago that the role of microbiome was recognized, for example, and even now it's contentious. Conversely, scores of epidemiological findings have had nice physiological explanations that turned out to be much more complicated, like those involving saturated fat, cholesterol, and carbohydrates. DHA, omega fatty acids, etc. are similar. Physiology is complex enough that you can accommodate just about any finding.
To carry this a bit further, it can be problematic going in the other direction too, from physiology to populations. Some of the anti-sugar advocacy, for example, was rooted in lab studies that neglected the effect of fiber in digestion of fruit, so you had people advocating that whole fruit consumption be avoided based on incomplete understanding. It's hard to argue that unprocessed whole fruit is undesirable on the basis of observational nutrition studies. Someone looking at the wet lab data and advocating abandonment of whole fruits might have done well to look at those observational studies to see why different trends were occurring.
I'm not saying that tying one level to the other at some point isn't necessary. I just think one or the other level can't be dismissed out of hand just because things don't map onto each other initially. It's possible that one level provides clues that the other is missing; it's also possible to come up with plausible but wrong bridges between the two levels.
I think the depth of knowledge is very uneven. We're not sure how Tylenol works. (Disclaimer: I work in software, not bioscience)
At least, placebos don't harm the user. There's evidence paracetamol is harmful. https://ard.bmj.com/content/75/3/552
And dosages higher than 4g/day are known to destroy the liver. Paracetamol overdose is one of the most painful way to kill yourself. Its abuse being freely sold over the counter makes it the number one cause of liver failure in the US and UK. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1403265/
>Paracetamol’s toxicity is also the single biggest cause of acute liver failure in the United States. Cases have been rising for six years, according to a study published in December (Hepatology 2005;42:1364-72). By 2003, the drug accounted for just over half the cases of acute liver failure, and about half of these cases were the result of unintentional overdose.
It boggles the mind the substance has not been put under harsher control yet.
For myself, until you can tell me by what means a particular food produces the claimed outcome, I dismiss your epidemiological nutrition study.