Yeah, that's also a bit weird. Not that she ships them but that it seems to contradict the "why do you adults CARE so much about the sexuality of characters from a children's cartoon" position that some of her tweets sort of imply. Like obviously they're adults, but it's not all that different.
Though she also seemed to say that it was fine for teens to like/draw porn of Star and Marco, just not anyone who's an adult and who may interact with teens. Which kind of feels weirder to me in a moral sense, saying some cartoon porn is fine but not others, even though of course teenagers are going to be having sexual thoughts too (and to some extent that's reflected in the actual show).
Like, it's just an adult younger than she is making mildly sexual jokes about a cartoon that's kind of done the same thing. Not like he's a fucking guidance counselor or something.
But yeah, I agree with you. Her work on the show has been among my favorites this season.