Yes - where did you read that? Regardless, narrative aside, the editing clearly shows that the rising scene was not supposed to be there and the transition was supposed to be straight to the McBain ranch.
Leone interview in Diego Gabutti's "C'era una volta in America" (page 37) , when he talks about OUTITW: "People very often ask me whether my personal print of the movie contains scenes which had not been added in the final theatrical release" he said grinning "You see? It's like everybody wants me to add a little piece to it..!"
But I think the definite answer about missing scenes in OUTITW is in Franco Ferrini's book "L'antiwestern e il caso Leone" published in 1971. There is a part of an interview with Leone dedicated to cuts and missing scenes of all his westerns, and concerning OUTITW Leone says (page 42): "The scene with the laundry owner's wife and the sheriff is missing, another one in the barbershop, which was particularly funny" The interviewer then asks about the massacre scene (Morton's train) and Leone says: "No, that one I left out on purpose, it was more important to show the result rather than how it happened".
On page 43 Ferrini writes: "It should be kept in mind that Leone's personal print is slightly longer than the theatrical release. It has two scenes which were not added. The first one showing Harmonica rising after being wounded at the train station. This scene was not in the original script and we publish now the description based on Leone's personal print. The second one is about Brett McBains hunting scene with his son Timmy; it's much longer and detailed compaired to the commercial release.
Now we look at an interview with Scorsese - where he says Leone gave him his personal print of the film:
When did you meet Sergio Leone for the first time?
It was at Cannes in 1976, during a dinner at the Oasis, the year when Taxi Driver was competing. There was Costa-Gavras, Sergio Leone, both members of the jury, I, Robert De Niro, Paul Schrader, the screenwriter of Taxi Driver, Jodie Foster, Michael and Julia Phillips, producers of the film. Paul Schrader had toasted Leone to thank him for having toured with Once Upon a Time in the West one of the greatest westerns in cinematic history. We had arrived two days earlier in Cannes and depression we had earned. Tennessee Williams, the jury foreman, told the press he did not like at all Taxi Driver, he was too violent. At dinner, Sergio Leone and Costa-Gavras told us they liked the film. We thought Taxi Driver could still win a prize, perhaps for his screenplay, or its actors. But it took the Palme d'Or! And that is thanks to Sergio Leone.
How has your relationship with him?
I lived partly in Rome between 1978 and 1981. I saw him regularly. Particularly at a luncheon at his home December 31, 1979. I met his wife, his family, met the set designer Dante Ferretti, with whom I will work later on The Age of Innocence, Casino, Kundun, Gangs of New York, Aviator and Hugo Cabret. He knew how much I loved Once Upon a Time in the West, he gave me his copy of the film. It is this copy that I projected in 1980 Film Festival in New York. It was the first time I spoke publicly about the crucial issue of the preservation of films, and more specifically the question of color, which happens if the coils are not kept properly. When Sergio Leone came to New York, I offered to come to dinner with my parents who still lived on the Lower East Side in a building without elevator. We went with Elio Petri (the director of The Working Class Goes to Heaven, Golden Palm at Cannes in 1972). He especially liked the Sicilian cooking from my mother, very different from Roman cuisine to which he was accustomed. And my mother was sensitive to his knife and fork!
So it is fair to assume, Scorsese was working under the assumption that his print was the correct version since it was given to him by Leone, but as we can see it was not the theatrical release.