Oh yeah, no one is disputing that.
Kala’s human DNA began a slow and painful process of conversion into monstrous HNA, causing organs to cease function or for her to grow new ones. It then wouldn’t be incorrect to think that her genitalia (if that’s what you’d still like to know about) would transform or disappear altogether as the mutation progressed.
Abe stated that, while asleep, Kala had spoken in a raspier voice, somewhat like an old man. When incapacitated and weak, Kala shouts out crazy things, speaking about how the monsters are right and they are bringing order. This can be seen as the monster breaking through to her mind for brief moments to attempt to dissuade the hunters from their assault. The monsters see this as a reasonable and logical course of action; we do not.
You seem to be thinking that the glowey glowey Kala in the Kali’s skull is still Kala fully intact, but you have to realize that Kala’s mutations didn’t grow over her flesh, they grew from it. Kala’s actual flesh became monstrous, and she slowly grew out from there. What we see in the Kali’s forehead could be Kala’s human nervous system glowing with monster conciousnesses energy, or it could be her “soul”, ikr any number of things. But you have to remember that the Kali grew out of Kala, not over. Kala’s real skin and organs and eyeball weren’t under monster flesh, they were becoming monster flesh.
Therefore, if the monster didn’t find her kidneys (I think that’s what she said were dissipated) relevant enough for her design, and since the Kali was based off of the five monster models found on Shear, I doubt she would keep her genitalia when the five models she was base on didn’t.