So, originally I thought that in Ancestor times on Beta-Alternia, Queen Ferrari wiped out all of the red blood trolls leaving Signless as the sole survivor.

But it now sounds like that it was the lime green blood trolls and that Karkat was always a genetic mutation in blood.

It is either that, or Anti-Jegus “won” and in the reset the red-blood trolls were kept while the lime-blood ones were eliminated.