I think Nathaniel is one of the more recent retcons and earlier versions suggested he might have been descended from Doom, but you're not wrong about all the "it was a Doombot all along" twists whenever the character was killed or otherwise defeated. Time travel in general means for paradoxes like that where a character can die before they first meet the people who end up being part of his death when the timelines involved don't run parallel all the time.