The plot elements of this story are callbacks "Cartman Finds Love"(S17E07) and "Tweek x Craig"(S19E06), making it a semi-sequel to those past episodes of South Park. And funny enough, if that becomes the plot of the Season 21 premiere, it'd be on Kaworu's birthday! How's that for a coincidence?
Assuming the current season of South Park is going to have a serialized story arc like last year, I think they should have it revolve around satirizing various anime and elements of the fandom. For instance they should do an episode where Cartman tries to stop an interracial young couple out of fear that their love will anger an alien deity who would come and destroy all human life on Earth, playing on how NERV was trying to prevent the ""forbidden union" of an Adam-type being and a Lilith-type being that would trigger the Third Impact. Cartman would deliberately misinterpret Evangelion as a cryptic cautionary tale about the dangers of interracial love and coexistence, using it as inspiration for a falsified "holy" text of his fabrication, not unlike the Dead Sea Scrolls, which justifies his racist beliefs, such as "Blacks must belong with blacks, whites must belong with whites, etc.".