Dark mode simply makes sense. Black pixels == no light == no photoreceptor stimulation == the default state. The fact that we used to blast our eyes with near-fully lit displays is a historical artifact of the early days of graphical computer interfaces. I find it annoying (and potentially medically dangerous to some people) that certain actions result in a short white flash while the content is rendered. Mostly happens in web-related apps.
Light mode is masochism mode, with just a few exceptions: e-ink, highly lit environments (that are uncomfortable to work in anyways), people with vision problems that tolerate light-themed UIs better, and weirdos who enjoy staring at a flashlight. If you're gonna use that, might as well just turn down the screen brightness - but I agree with the author that perhaps a middle ground "gray theme" would be better, if slightly less attractive to UI designers.
You could equally say "we're evolved to hunt during the daytime, where you scan the environment when the surroundings are bright."
> people with vision problems that tolerate light-themed UIs better
Astigmatism is very common.
Light mode constricts your pupil more, which means less eye strain for the eye when focusing because of the better depth of field. Also, black pixels != no light except in technologies such as oled, but most laptops are backlit lcds.