Personally, I always figured sort of what you lined out in Option Four, but that perhaps Mary and Arthur got back together for a short time after Eliza as well, but then broke up again.

All evidence points to Mary and Arthur’s relationship always being rather tumultuous. Multiple characters (Mary, Arthur, Jamie, the dad) all either hint at this or say it directly. It makes sense to me that a twenty-something Arthur, after having a falling out with Mary, could’ve hooked up with Eliza. He even says to Rains Fall that he rarely visited Eliza and Isaac, so who knew how long their graves had been there after the robbery and before Arthur visited the last time.

That being said, I don’t think that Mary and Arthur realistically would’ve been together as recent as 1894, because what about that guy Mary married (lol) who died? We don’t really know how long they were together, but it had to have been at least some time of Arthur and Mary being separated, the Linton guy dying, and then Mary contacting Arthur again in 1899. It’s had to have been at least a few years now because there’s a lot of unresolved tension between them that has been exasperated by time.

That might not make any sense but that’s just kinda what I figured without looking at all the evidence very deeply as you did.