Takeuchi has her own ideas for Super S, Neherenia Arc, and Stars which she planned for the Anime but never in the manga like the wristbands/wristribons for the Eternal Senshi and Galaxia being Sailor Chaos.
I am speculating here, but I believe Naoko Takeuchi provided TOEI with a guideline for SuperS and Stars, respectively. I personally do not believe that Naoko’s ideas, those from the manga, were rejected because the anime ended
before the manga was concluded. In other words, Naoko was still crafting the last chapters of the manga after the anime ended.
Another important aspect for fans who believe Crystal’s first season deviated from the manga: it was only
after the “Sailor Moon” manga was concluded that Naoko had time to finish the “Sailor V” manga—and while doing so she had time to briefly revisit the Dark Kingdom arc by suggesting a romantic affair between Sailor Venus and Kunzite, an idea that had been subtly implied in the first arc of “Sailor Moon” (the colored illustration), but not fully developed.
The last chapter of “Sailor V” heavily implies a relationship between Minako and Kunzite—and the last panels of the “Sailor V” manga should be considered when criticizing the senshi x shitennou pairings.
Other than the pairings, the only thing that Crystal did differently was Beryl’s death. As much as I would like having the same scene from the manga, I suspect they changed because there is actually blood, it is a grisly scene that doesn’t match Crystal’s shoujo aesthetic, and we already get to see Usagi stab herself (and Mamoru) with the same sword in Crystal. I think we won’t see Usagi coughing blood in Eternal for the same reason.