The one place it isn't the supreme paradigm is in industry. Oh, it used to be—think of the motion-study experts of the early 20th century. They were extremely reductionistic; every motion was studied in an effort to make every motion efficient. But all that started changing with Deming and his marble experiment. In a nutshell, he showed that reductionism wasn't the answer; the system was bigger than the sum of its parts.
Sure, the change didn't happen overnight, but the corner had been turned. The dominant industrial paradigms of today, Toyota Production System and the Theory of Constraints are systemic approaches. Another good example is Peter Senge's Fifth Discipline approach to problem solving. The result has been the dissolution of what is called "silos" in the industry. Silos are narrow concentrations on your specialty to the virtual exclusion of other aspects of an organization; they are named after the round silos found on farms. The assumption behind siloing is that nothing outside my specific area has any affect on what happens. Right! It is extremely reductionistic.
So why did atomization fall out of favor in industry but nowhere else? Simple; follow the money!
In industry, throughput means more income (this is hugely simplified, but bear with me!). When one part of an industry adopts a systemic approach, their throughput increases and their costs drop. They can afford to sell things for less than their competitors with no reduction in quality. Money talks! Pretty soon, their competitive advantage is adopted by others.
Now look at the medical and food industries. Keeping people sick and fat is good for business. Healthy, fit people don't eat as much junk food. They don't need prescriptions. They don't get sick as often. They don't guzzle carbonated, sugared beverages.
In short, they don't contribute to the bottom line of the food and medical industries...no conspiracy theories needed. In our money-oriented society, where results are measured by quarterly Wall Street results, there is no incentive to keep people healthy via a whole foods, plant-based diet.
I could go on, and probably will over the next few weeks...