Although gaining muscle is much healthier than gaining adipose tissue, the implication of the article (and an abundance of empirical evidence) is that eating itself is a stressful process. Eating is the vector through which you expose yourself to oxidative stresses and pathogens. Eating less but still meeting your caloric needs would mean minimizing exposure to these risk factors.
At the same time, humans in good shape are definitely healthier, and too much calorie restriction can lead to malnourishment.
There's a sweet spot somewhere, proponents of calorie restriction are basically saying to err on the side of eating less.
That's very misleading logic. You make it out that your organs working much harder is a bad thing in all cases. That's not true.
When you exercise, your organs work much harder. Yet it is much better to exercise and have your organs work harder than to not exercise at all.