Absolutely, yes.

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.

In a sense, yes - to build up your muscles they must first be broken down, a cycle which is going to create some amount of stressful churn. If you think about any machine, a higher operating energy/intensity generally correlates to faster breakdown.

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.

I read somewhere that physical activities are stressful but then make your body more resistant to oxidative stress, which may explain the paradox of physical activity like lifting improving health and longevity. So maybe caloric restriction compared to slight calorie excess+muscles might end up being relatively equal in terms of longevity

whether you are muscular or skinny, you have the same set of organs. The fact you are 30 percent bigger in mass means all your organs (heart, liver, kidney, muscles, ...) are working much harder than if you had less mass.