All doctors recommend eating well. But none of them actually knows what eating well means. Or, rather, they might think they know, and still you get ten conflicting answers.

Diet and health is incredibly complex. Not only is it about which nutrients we get for our body, but also which bacteria live in our gut and which nutrients they need and in what concentration, so that the balance stays the same. A healthy diet is basically about trying to feed an ecosystem.

Definitely. However, this has been used to market a myriad of so-called health products that are far from ideal.

I follow a carnivore diet and have always been a bit scared of messing up my microbiome, while finding it quite strange that I defecate non-negligible amounts of waste, once a day on average.

Only recently has my knowledge gap been filled when I found out that our microbiome can survive solely on amino acids. In fact, all this "gut-brain axis" stuff regarding the production and/or catabolism of neurotransmitters by gut bacteria only makes sense if bacteria can ferment amino acids. Thinking that some bacteria strain can produce neurotransmitters from fibre is an insult to intelligence: where does the nitrogen come from?

in most cases it's nitpicking. While an apple might be 6.48% better than a pear for a certain person at a certain time, eating an apple is still way better than an order of french fries.

We're talking about basics, getting all the vitamins and nutrients needed for a healthy body. Exercise, eat about 5 servings of fruit and veggies a day etc ....

It might be nitpicking, but there are many, many subtleties that depend on individual aspects that exhibit a high level of variability.

Take, for example, minerals (electrolytes). Calcium absorption is greatly affected by the rest of your diet (fibre intake, phytates, oxalates and other antinutrients). A person eating a high amount of nuts containing calcium might absorb less than someone eating only meat (fish), which contains much less calcium by weight, but none of the factors that negatively affect absorption.

In other words, RDAs are not fixed. Someone on a purely carnivore diet needs less than 80 mg of magnesium per day, while someone on a vegetarian diet might need over 500 mg to maintain magnesium status.

Pardon the math analogy, but regarding the direct comparison of different food items, it is clear that some order relation can be defined between them (e.g. an apple is better than a serving of fries), but that relation is far from being complete. Is an apple always healthier than an rib-eye? Are they even comparable? Is a bowl of steamed rice healthier than a slab of butter?