I would guess, and I have no real idea, that the novels are sequels to the whole trilogy while the comics act as a sequel to The Good, the Bad and the Ugly, set, I guess, before the rest.
I mean, are you sure that the present day of the film is set around that point? Referencing that event, even showing it, doesn't mean that the present day is set there. You're probably right, but a lot of timelines seem to suggest 1864-1865.
Dollars Trilogy (The Man With No Name)
1862 - The Good, the Bad and the Ugly (1966)
1872 - For a Few Dollars More (1965)
1973 - A Fistful of Dollars (1964)
There's also comics and novels. It's definitely canonically the same character.
I've seen people say that Mario and Sonic at the Olympic Games isn't canon due to... uh... the fact it's a crossover? I don't personally understand that, but maybe there's a statement making it a unique crossover universe.
The actress pretty much said that she was playing a younger version of the movie character, and the Misery's Love book doesn't exist in the novel but does in the show and movie.
If Mystique isn't explained, I'm just going to say that the Phoenix Force resurrected her. It wouldn't really be that far fetched, as far as off-screen, unexplained continuity issues go.
https://marvel.fandom.com/wiki/James_Howlett_(Earth-807128)
I actually kinda like that the original Old Man Logan lived past 2509 and somehow managed to regain his healing factor. It's a little funny that the version of the character that ended up in Earth-616 and eventually died is actually a...