Something to keep in mind when reading movie directors interviews: they're also read by producers / investors. Regarding Villeneuve, he wrote an open letter criticizing the studio choice to release Dune on both cinemas and HBO Max. Putting Zendaya at "the protagonist" for the next part could be a nod at the studios to sell his project better (we all know why).
Could be a lost in translation thing since the interview was written in italian but I don't see Villeneuve rewriting entire parts of the book just to push Chani in front of every other character. I could be wrong though, selling film projects that are not capeshit / remakes / franchises / reboots in this age is getting utterly hard, especially science-fiction stuff.