You're kinda quoting the interview out of context here. The team is talking about how they made most of these core decisions at a residential in the winter after the release of Shadowbringers, and came up with the outline of stuff like Meteion during that event.
They're saying the same thing about deciding who the final boss should be. At the residential they realized that no one particularly wanted it to be Hydaelyn or Zodiark, but nevertheless they hadn't made any firm plans prior to that point, meaning the idea of it being one of the two was definitely on the table in theory while ShB was being written.Ishikawa: After Shadowbringers released, around the end of 2019, Image Studio [note: the CGI studio within Square Enix that produces the high-quality cinematics in various SE game] had to be provided with storyboards. In autumn and winter of that year, we went on a residential together in order to decide the main points of the story for the next expansion. But the problem was… we’re used to the writing process, and so feeling that “here and here are the remaining parts of the story we have to talk about, so let’s accept the rest”, the residential went very smoothly. I was in charge of filling in the details of the story elements, but when I looked at the structure of the content again, I thought “this might be okay for just another expansion, but if this is labelled the ‘finale’ is it really okay?” So I reworked the story from the plot outline. The end result was ready 2 days before the deadline.
Interviewer: In the plot at that point, were elements such as Meteion already included?
Ishikawa: The name Meteion wasn’t there yet, but the base form of what she became had been decided.
Edit: Actually, re-reading this, they could not be talking about last bosses at all? But it seems like they're still saying that which one would be antagonistic wasn't clear. I remember it being more explicit - I need to read the actual interview again and not just cite these reddit notes. I think there was another which also touched on the topic briefly more recently, where they discuss when they conceived the Final Days and Amaurot concepts...
I can't prove a negative. They never discuss the intentionality of the Sundering in Shadowbringers as it pertains to anything other than Zodiark at all.------ Oda explains that the devs seek to balance delivering on players’ expectations and also having unexpected developments. Players were already expecting to fight Hydaelyn and Zodiark, so it was debated among the devs whether to deliver the fights straightforwardly, or have a surprise development where one of them would take over the other and fight you. In the end, the team decided to go for the straightforward route, and the last boss would be something unexpected.
Yoshida: At the residential no one thought Hydaelyn or Zodiark should be the last boss.