Maybe because she's the best example of their agenda with Astarion? Karlach is a motherly character and the Spawn route is basicly becoming Astarion's mum deciding things for him and his great protector. If she goes with AA they show him being very unhappy about the fact he cannot turn her into a vampire and saying hurtful things towards her (which is basicly the game proving how incompatible they are - she is so goody-two-shoes that her whole body protests against the transformation into an evil bloodsucker, unlike in all the other scenes where she turns blue).
Either way, it's the game creating it's own fanfiction because Karlach would never allow him to ascend. Same as Astarion would never stay with a mind flayer but when you play as him you can make him kiss her tentacles.
