The difference is between the known interaction of chemicals that have existed for a considerable time as an agricultural product and synthetic chemicals that have unknown interactions.
Organic pesticides and their interactions aren't that well known... hell, all around the interactions of most of the foods people eat, gene expressions and even gut flora leave most data almost meaningless.
Eat food you make from mostly whole sources, avoid sugars (especially refined), avoid grains (especially refined), avoid refined seed/vegetable oils... do those things and you're still doing better than most of the population, even if your veg and meat aren't completely clean.
Toxicity and microbial selectivity are not the same. Whole food's positive biotic selectivity benefits could be negated by toxins present. I'm not really sure what "doing better" means bc it depends on the individual. Less likely to have endocrine disruption? Cancer risk? Better cardiovascular health? The optimal diet depends on your risk profile.
Take any 10 people and give them trace amounts of X (whatever X is) over the course of 5 years... they won't respond the same. Some will go through it easier than other. Some may have allergic response, others won't.
As for the general advice to avoid sugars, grains and seed oils. These are all things whose consumption correlates the most to increases in heart attacks, obesity, dementia and many related diseases. They are absolutely not required for anyone and for most of the population consumed in quantities that cannot be justified as healthy or safe.
Eating lots more vegetables (in scale and variety) and some more fruits (keeping sugar manageable) generally corresponds to better health. Regardless of other macro nutrition (though I feel that meat, eggs and fish are fine). "OPTIMAL" historically speaking has mostly come down to cost and availability. Optimal for man, in general comes down to what could be raised, gathered, hunted or foraged relatively locally. That would include regular periods without food, and a few in excess.
Eat food you make from mostly whole sources, avoid sugars (especially refined), avoid grains (especially refined), avoid refined seed/vegetable oils... do those things and you're still doing better than most of the population, even if your veg and meat aren't completely clean.