To be fair, that "plot to betray them" thing happened at the end of Frenemies, whereas "Chrysalis obeys no one" happened before the Villain Song.
...I wouldn't doubt Chrysalis was already seeding plansthe beginnings herof miplands of "betray him" by that point, in her mind, though, if only in the "fantasize" stages because she didn't have a discernible way to go about it.