I think that with the debate over whether or not Karkat is Kankri's father, you have to take into consideration that Karkat did the ectobiology thing, like John. Wouldn't that make him Kankri's son?

Not necessarily. We don’t know for sure who is who’s parental figure regarding the trolls. It really depends on who was cloned and who was ectobiologically made.  We assume that since the Beforans came first that is how it works out with the Beforan ancestors being the parents. 

We can’t be sure really.

~Mod T