The people who write the story by their own admission rushed to wrap things up earlier than planned, cut out an entire expansion and ignored the established narrative from one expansion to the next. Furthermore, just because the development team say something it doesn't mean everybody has to agree with their take.

Yoshi-P could write a story about how Y'shtola woke up one day and decided to become a serial killer that specialises in burning down orphanages but come up with a contrived excuse to say that she's actually a good person because those kids might have grown up to be a threat.

Which isn't much different from the laughable and pitiful excuses used to try and shield Venat from criticism. Genocide isn't suddenly acceptable or a necessity just because some pretty woman is the one partaking of it. Furthermore, video game developers are very far down the list of people who I'm interested in hearing lectures on morality from in the first place. Endwalker isn't exactly Matsuno tier in terms of quality and consistency. It has many holes - and much like with the holes in the Sage icon, there's now a panicked effort to try and cover those holes up.