Nutrition science is in its infancy. It's clear that the complexity of the interaction of food as it is digested and interacting with our organism has barely had the surface scratched. Also, if you look at the rise of processed foods along with obesity, diabetes, and other health problems that have increased over the past century it's clear that there are some serious problems, and they haven't been explained conclusively by this or that macro-nutrient trend.
So given the state of the evidence, a vague evolutionary assertion that whole foods are generally healthier than a distilled diet of completely isolated nutrients is not granola flag-waving woowoo nonsense, it's a perfectly reasonable belief based on imperfect evidence.
Put another way, the idea the ability to construct a perfect diet given the knowledge we have is likely to fail due to the overwhelming number of unknown details that simply aren't an issue when you're eating whole foods.
If this guy wants to experiment on himself than I'm happy to reap the benefits, but I do believe it's risky. Let's not whitewash common sense just because of "a lack of data". The fact that we have imperfect data does not make all approaches equal, and the fact that this guy is an engineer and wants to follow a scientific approach does automatically make his ideas superior to someone who holds certain nutritional beliefs for slightly more hand-wavy reasons.