What's interesting to me is that this is the introduction paragraph to just about all the different ways of eating that are being promoted.
We all agree on the basics of the problem - commercially available foods bad.
The solutions are varied and contradictory, and nobody agrees on "the science".
A doctor recommended I read a book on plant based diets (How Not To Die), when I told him I had gone to a zero-carb diet. I did. I was surprised at how much I agreed with in that book, or had seen already with different conclusions reached.
I think this has to be where self-experimentation comes in, and maybe a little common sense and learning. If your own experiment makes sense to you, based on your understanding and your own research, then try it. If it doesn't work, change something.