It's the default in many recent systems despite historically not being so. It's a bad name for hinting the natural is the most common option or that the alternative is any more unnatural when it's just a matter of perspective. It's also not a descriptive enough name to be easily understood.

About the historical reason, my guess is that the mouse has always been the pointing device. Following this reasoning, when you scroll "down" you're indicating you want to expand the bottom of the screen. Auto scroll when present also uses this observer perspective over the content's ("natural") one.

Apple, for one, because not only do they default to this but there's no option to change it separately for the mouse wheel vs touch pad without third party software.