I mean, first of all, I really hope he is not gonna call it Dune Messiah, but Dune Part Three. The way Part Two is set up and how it is different from the book it is obvious that they were setting up a trilogy pretty much from the get go.
There are some statements that I found very interesting regarding the studio's decision to greenlight Part Two. Everyone in the cast and crew made it seem like it was uncertain until the very second they announced Part Two in 2021. However Villeneuve said in a recent interview that even
while they shot Part One (!) Legendary secretly ensured him that they were going to go forward with Part Two, no matter how well Part One will be doing at the box office. So yeah, I'm not believeing anything he says now
And after his statement on this I even believe they were going to do three movies from the very beginning tbh, especially with how Part Two feels like the middle movie and is certainly set up and designed that way as a movie and story. I'm sure Part Three is gonna be great and they're 100% gonna make it.
And again, I really hope it's not gonna be called Messiah. The film is gonna have to be kinda different from the book the way they set things up in Part Two, not the least Alia's (Taylor-Joy's) age, so not calling it Part Three to conclude a trilogy would be kinda weird. Dune Messiah is also a little trippy, If I would bet on it I'd say that we're gonna see a bit less of those heady themes and more of war in the third film, the ending of Part Two may hint at that, which is not shown in the book, but sort of happens off screen and is only being talked about from the far.