Not particularly. In sum, RDR2 draws on elements that do have parallels, but with several glaring caveats, the first being of course that it is a form of popular media and presenting Western tropes that reflect more on the Western as a genre in film and paper, and the second being that what can be said to be drawing on reality isn't drawing on 1899 specifically, but the history of the West generally.

I'm borrowing a bit from previous writings as well as expanding at points, but I would first address 1899, which is something of an important year in the history of Civil War remembrance, only a year after America's trouncing of Spain, a conflict which is of central importance to the self-image of the South allowing a renewed idea of shared military heritage. The conflict gave a common enemy to "emphasize America’s Christian and Anglo-Saxon heritage as the source of national cohesion." A popular anecdote from the Spanish-American War is Confederate veteran Joseph Wheeler, in the heat of battle, yelling out "Come on boys, we've got the damn Yankees on the run!", and whether true or not, the fondly humorous way it is constantly retold certainly helps to illustrate how these two conflicts "reaffirmed national unity and further enabled this vindication of the South". Even if he didn't say it, the choices of him and Fitzhugh Lee as Major Generals were apparently quite deliberate on the part of the military authorities looking to ensure more Southern support for a conflict that Southern leadership was initially somewhat tepid about.

Writing of the war as background to the Lost Cause, Gaines M. Foster notes:

Southerners who sought both to vindicate the Confederate soldier and to reunify the nation might have staged the Spanish-American War if it had not come along when it did.

While Caroline Janney goes further in emphasizing that:

For white southerners, the war did more than foster reconciliation. It also vindicated the Lost Cause. [...] By highlighting their own fight for "liberty" [...] white southerns could simultaneously claim loyalty to the US flag and to their Confederate heritage.

As I said, for this part I'm cribbing, and I talk about the broader narratives of reconciliation here but the important point to be emphasizing is that the late 1890s were a focal period for sectional reconciliation, although only part of a wider narrative, one that fostered the growth of the 'Lost Cause' into the conventional story of the war, not to mention undercut the place of African-Americans in that story in the interests of white reconciliation.

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Now, as for the more central matter here. The short answer is that No, there was not a large guerrilla movement like the Lemoyne Raiders with Confederate sympathies present in 1899. As per the above, so called 'unreconstructed elements' persisted for decades, but they didn't last a generation (and as I recall from the in-game lore, isn't there a newspaper saying the Raiders aren't a continued institution, but only recently started up? Neither here nor there really since there wasn't something like this either way). But this isn't to say that there aren't parallels to be drawing on. The first of course is simply prior media, many Westerns incorporating the Civil War in, either as a backdrop to the action such as in The Good, the Bad, and the Ugly, or providing background for a character in the post-war period, such as The Outlaw Josey Wales or Seraphim Falls.

It isn't only the realm of fiction however, and the impact of the Civil War on the West - and especially the American mythos of the Wild, Wild West, can't be understated, for which I'll focus on the outlaw Jesse James, generally remembered as a (in)famous western bandit, but one whose exploits, especially in the years immediately after the war, absolutely need to be understood in that context, and more broadly speaks to the form of post-war Confederate sympathies that the Lamoyne Raiders represent, even if a bit too on-the-nose and far off in the future.

During the war, James and his brother both served in the Confederate forces, riding with the infamous group of bushwackers led by William Quantrill and William "Bloody Bill" Anderson. The most infamous of a broader collection of generally infamous such partisan raiders, which carried on a legacy that predated the war into the brutal, if localized, clashes of 'Bleeding Kansas', 'Quantrill's Raiders' were responsible for some of the worst atrocities of the war, such as the Lawrence Massacre and the Centralia Massacre, in many ways using the war as a cover for lawlessness, something which would eventually lead to the Confederate government essentially disowning many of these groups, only leading to them being further loose in their respect for the norms of warfare (it must be noted that the comparable 'Jayhawkers' in line with the Union were not always well-behaved either, but that is its own matter).

Anderson and "Bloody Bill" would both not survive the war, but the James brothers and many other raiders did too. Some surrendered, but unlike regular soldiers, these men were not to be accorded the same rights that most defeated Confederates received, and didn't trust Union claims of clemency. Jesse is believed to have attempted to but was shot when he rode up, which of course would do nothing to make him think otherwise. Some slunk home in secret, but many others simply... didn't surrender. This was the genesis of the James-Younger Gang, a collection of former Confederate guerrillas who had no interest in turning themselves in and, without a country to fight for anymore, went into business for themselves to to speak, although it should be emphasized again that, given the nature of groups like the Raiders, who existed on the fringes already, transitioning to bank-robbing was not all that different than how they had conducted themselves during the war either. They were not the only bushwackers who continued after the war, but would soon be the most famous.

The 1869 robbery which would bring them to real prominence saw them shooting down the teller who had mistaken for the man that had killed "Bloody Bill" - an identification he was mistaken in, the man ironically being a leading Democrat in the local community - and the memory of the war was of great importance in many other ways, both how they were seen, and how they saw themselves. An excellent example would be the writings of John Edwards, a newspaperman who was instrumental in crafting the 'Robin Hood'-like aura that surrounded James, and was himself a Confederate veteran who had ridden with Jo Shelby. In his 1872 article "The Chivalry of Crime" on a Kansas City robbery, Edwards wrote poetically that:

There are men in Jackson, Cass, and Clay - a few there are left - who learned to dare when there was no such word as quarter in the dictionary of the Border. Men who carried their lives in their hands so long that they do not know how to commit them over into the keeping of the laws and regulations that exist now, and these men sometimes rob. [...] These men are bad citizens but they are bad because they live out of their time. The 19th century with its Sybaric civilization is not the social soil for men who might have sat with Arthur at the Round Table, ridden at tourney with Sir Lancelot or won the colors of Guinevere. [...]

Such as these are they who awed the multitude on Thursday. [...] What they did we condemn. But they way they did it we cannot help admiring. [...] It was as though three bandits had come to us from the storied Odenwald, with the halo of medieval chivalry upon their garments and shown us how things were done that poets sing of.

Edwards was hardly alone, such as the words to this folsong published just around the time of James' death:

Jesse James was a lad who killed many a man.
He robbed the Glendale train.
He stole from the rich and he gave to the poor,
He had a hand and a heart and a brain.

Praise such as this was all words which the gang apparently matched, Edwards publishing a letter he claimed was from them, although some believed he wrote it himself. In any case, not only do they echo the themes of chivalry, but they more openly laid out the politics of their actions, setting themselves up not as common thieves, but unreconstructed Confederates trying to continue the right against the Grant Administration and the Republican Party:

Some editors call us thieves. We are not thieves - we are bold robbers. It hurts me to be called a thief. It makes me feel like they are trying to put me on a par with Grant and his party. We are bold robbers, and I am proud of the name, for Alexander the Great was a bold robber, and Julius Caesar, and Napoleon Bonaparte, and Sir William Wallace. [...] Please rank me with these and not with the Grantites. Grant's party has no respect for anyone. They rob the poor and rich, and we rob the rich and give to the poor. As to the author of this letter, the public will never know. I will close by hoping that Horace Greeley will defeat Grant, and then I can make an honest living, and then I will not have to rob, as taxed will not be so heavy.

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