I think it feels irrational because these high protein, low carb diets are really meant up be weight loss diets, not the diet of an active human with healthy fat and muscle levels. In that case, whole grains and vegetables, fruits and the like along with the supplemental meats and nuts are normal. If you're genetically disposed, throw in some whole fat, no sugar added dairy.

I think all this confusion arises because what is good to eat is different between an obese person who works a desk job, a bodybuilder, a skinny 5-miles a day runner, and everyone else. People advocate one diet without considering how it'll interact with someone's standing fat and muscle levels, cardiovascular health, and insulin sensitivity.