The Villeneuve Dune(s) can be broadly interpreted as one of the two possible futures Paul sees in the original novel
Spoilers below for Dune Part Two. (And for the original novel, but that's been out since the 60s.)
He had seen two main branchings along the way ahead--in one he confronted an evil old Baron and said: "Hello, Grandfather." The thought of that path and what lay along it sickened him.
The other path held long patches of grey obscurity except for peaks of violence. He had seen a warrior religion there, a fire spreading across the universe with the Atreides green and black banner waving at the head of fanatic legions drunk on spice liquor. Gurney Halleck and a few others of his father's men--a pitiful few--were among them, all marked by the hawk symbol from the shrine of his father's skull.
"I can't go that way," he muttered. "That's what the old witches of your schools really want."
Obviously the Doylist explanation for why there are differences in the new films is that the original book is 60+ years old and has certain elements no longer in cultural vogue that were adapted out or altered to better fit modern sensibilities, and I'm all for that. But I did find it interesting that there is an explicit moment at the end of Part 2 where Paul confronts the Baron, utters the "Hello, Grandfather," line, and kills him.
This isn't necessarily because there is any one choice that Paul makes throughout the course of the two movies that leads here instead of to the jihad. In point of fact, most of the changes that drive him here are caused by choices made in the adaptations of the films.
The causal chain that leads to Paul undertaking the spice agony is his failure to predict the attack on Sietch Tabr, rather than his failure to predict Gurney's attack on Jessica; this is, of course, necessitated by the omission of the Harkonnen scheme in part 1 to impair Thufir's Mentat efficiency and potentially drive a wedge between Leto and Jessica by framing Jessica as the traitor. The final push that causes him to make the decision is, of course, the vision he experiences of an alternate future in which he didn't have to kill Jamis, with Jamis counseling him to climb as high as possible before the hunt so he can see as far as possible. (In other words, he ignores Stilgar's advice of not listening to the djinn.)
Similarly, his killing of the Baron is necessitated by the adaptational choice to keep Alia as a fetus so the audience doesn't have to deal with a two-year-old talking like an adult and killing the Baron, which they probably did because it would have been distracting.
However, I might argue that a Watsonian explanation for the film omitting the two-year time-jump lies specifically with Paul's decision to explicitly disavow the prophecy when Jessica undergoes the spice agony, and to explain to the Fremen that her survival is because of her Bene Gesserit training. He then attempts to secure his position with the Fremen through secular deeds, rather than letting Jessica carve a place for them with the BG prophesy.
This disagreement between the two of them causes her in turn to take a more active approach in cultivating Paul's status as Lisan al-Gaib, which accelerates the timeline of the Fremen being ready to submit to him. In turn, Paul focusing more strongly on guerrilla war against the Harkonnens accelerates the timeline of Feyd-Rautha being put in charge of Arrakis and cracking down hard in the north, leading to the aforementioned crisis point of Sietch Tabr being attacked without Paul's foreknowledge.
Notably, while we do see the shrine of Leto's skull in the film, we only see it in a vision; there is no moment in the movie where Paul explicitly finds his father's remains and enshrines them. Hence, going from a strict interpretation of the film's "text," this is not the future in which the legions are marked by the shrine, because the shrine doesn't exist. It is the other future. The compression of time means that Paul and Chani's relationship is much newer and more fragile and doesn't survive the strain of his apotheosis, and that's what sickens him most.
Of course, the "Hello, Grandfather" path also leads to the jihad, because Paul's tragedy is that his very existence was always going to lead to it, regardless of what he chose to do.
And Paul saw how futile were any efforts of his to change any smallest bit of this. He had thought to oppose the jihad within himself, but the jihad would be. His legions would rage out from Arrakis even without him. They needed only the legend he already had become. He had shown them the way, given them mastery even over the Guild which must have the spice to exist.
Obviously none of this passes explicit, close scrutiny, and is more of a fun "if you squint and look at it a certain way it kind of makes sense." I expect that the line was put in as a nod to the original book, no more or less, but making up head-canons like this is fun for me and if even one other person finds it edifying then I consider sharing it time well spent!
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