That argument makes no sense. It's like saying we evolved to walk barefoot, therefore shoes are bad for you.
Just because we evolved a certain way, doesn't mean that's the best way to do things.
My hypothesis is Dark mode is less light, and less light is better for your eyes.
But until there are scientific studies on the topic, who knows.
If you were walking barefoot all your life, you'd have strong feet, as evolution wanted.
Low light condition is actually awful for your eyes. I can use drive without glasses in the morning, but at night I really need them, because our eyes are designed for day light conditions.
And by better I mean (from the article): "Light Mode provides better performance in focusing of the eye, identifying letters, transcribing letters, text comprehension, reading speed, and proofreading performance, and at least some older studies suggest that using a positive polarity display results in less visual fatigue and increased visual comfort."