Could be that mortals becoming deities was a newer rule they implemented, possibly after losing several more gods (or even pantheons).
If that's not the case, it could mean the Dark One ascended from another world and that's why the details of his mortal days are unknown. Or perhaps he never was an ascended mortal and is instead the sole survivor of a purple aura pantheon. Though him apparently being ignorant of the other 4 Gates makes it seem likely he is indeed from the current world.