Suiting + that hand made shirt.
That fallacy really doesn't apply to biology. You can apply the same evolutionary adaptiveness principles to all sorts of things, such as food (i.e. people everywhere eating traditional meals are overwhelmingly healthier than those eating a industrialized Western diet, leading to the conclusion that "natural" diets and whole foods are better, at least until we can figure out why), sleep patterns, even weight training (barbell training is far more effective than machine training because it runs the body through its most "natural" range of motion).
Heavily-padded shoes absorb shock from impact. Barefoot, that shock would be distributed throughout the leg, and primarily absorbed by the knee, so if you have knee issues the padding is a good thing. For a lot of people, though, the padding can also screw up your gait when running or walking (if you heel-strike while running, a pretty easily solution is to switch to a shoe like the Free or go barefoot) and prevents a lot of the smaller stabilizer muscles in the foot from doing much of anything.
I'm not really saying that everyone should go without shoes, just to be careful of those running shoes with like an inch of padding. Just because it feels squishy and comfy standing still in the store doesn't mean it's better for you.
Edit: I'm also totally biased because I studied evolutionary anthropology as one of my majors in undergrad.
Seems like a lot of broscience, honestly. Exercise advice is one of the softest fields of knowledge out there. I'm not saying you are wrong or right, I just don't think approaching the subject in such certainty--nor appealing to nature--is the right argument to take here. It's a closed argument for an open, grey topic of debate.
After all, it's a fact that shoes increase top level athletic performance.