Ignoring the homeopathy nonsense, "whole foods" as they're generally referred to have the benefit of proving themselves through selection over tens of thousands of years. They are the baseline that we're working from, and in general the burden of proof should be put on deviations from that baseline.
Yes, there's been selective breeding, etc. But with the scale & pace of change in food "science" in the last 50 years moving at an exponential pace, there's little in the way of evidence that extremely processed foods are anywhere near as nutritious as "whole" foods.
Instead, there's a ton of anecdotal evidence to the contrary. That food "scientists" don't have anywhere near as robust an understanding of what it healthy & nourishing, and that when they try to break foods down to their constituent chemical parts and build something else from scratch, you get Frankenstein foods that are at their core unhealthy and detrimental to those consuming them.
To call the machinations behind modern food processing a "science" is woefully misleading. There are enormous gaps in knowledge, and if natural foods have proven themselves over a larger order of magnitude of historical time, we should be applying much more rigorous standards to deviations from animal-food relationships that have evolved naturally or at a much slower pace.
And you get people saying, "why should we require GMO food to be labeled? Prove that it's harmful" you have to look at the unhealthy relationship between big agribusiness money and studies saying GMOs are safe. We thought Lead in paint & gasoline were safe, we thought asbestos was safe, we thought dioxins were safe to be used as pesticides & herbicides, we thought tobacco products were safe. Until people started developing horrendous diseases & birth defects, and we learned they weren't. And even then, the manufacturers of those products continued to fund studies & propaganda campaigns to the contrary.