For starters, it is how the party stops looking for a cure once you arrive in the city. Even though this is where it would make sense, with the high level clerics and temples - not that you have access to them, since they were mostly in the northern district). Of course, there is Raphael, who in act one has promised to fix it all "like this" once you arrive exactly at this point. But in act three he offers you the hammer, which does not fix much. And if you are allied with the emperor, it doesn't even present a temptation. I think Orpheus, unlike the emperor, is actually in the artbook (though I'd have to check again), so perhaps originally he could have actually provided a cure.
I also never found an explanation as to why Gale detonating the orb in act two causes everyone to transform into mind flayers, but when he does the same in act three everyone is cured. It even reverses the partial transformation. I suspect some chunk of Gale's story is missing as well, because you can find information that in order to control Karsus' weave, you need the crown, orb and scepter. The scepter is however not in the game. And on the topic of Gale, you can learn by playing his origin that a god has the power to restore a mind flayer's soul. Yet Withers does not even mention it.
Then there is the ending itself. The dialogue that is required to avoid transforming anyone into mind flayer if you have Gale in the party and side with Orpheus is nonsensical. So is Orpheus transforming using the tadpole, or without it, depending on whether you have obtained the tadpole. The last of which I suspect was added, because shortly after BG3 was launched, WotC advertised a tabletop adventure where mind flayers could transform people remotely (I don't play p&p, so I only learned of this from the Larian discord).
