In my previous theory, I mentioned at the end that I would explain how and why Francis Sinclair, Red Dead Redemption 2's time traveler, was never intended to be a reference to the Epsilon Program's descendants of Kraff, the famous Emperor of the 4th Paradigm and also the GTA equivalent of Jesus.
Beta (IKZ):
During the beta, the Princess' side quest was indeed going to be a bounty-hunt type of mission; the player needed to search for specific clues to unlock the secret encounter at Van Horn's fence, and then Arthur/John took her to Annesburg's sheriff's office to complete the mission.
The Princess:
Isabeau Katharina Zinsmeister disappeared in 1884 from a remote hunting lodge (The Loft?) while on a private family excursion to North America. There are numerous theories on what happened to her: some believed she was murdered, some that she was abducted and kidnapped, although no ransom note has ever been received, while others suggest that she was eaten by wild animals.
References to Epsilon:
Her birthmark heavily resembles the birthmark identifying descendants of Kraff, a deity worshiped by the Epsilon cult in the Grand Theft Auto series. The date 1884 is also a nod to the Epsilon Program; Chris Formage visited Luxembourg in 1994. These are just references to Kraff's descendants as there is no actual proof that links one with the other. And it is not the first time that Rockstar has added characters with such birthmarks: Curtis Weaver and "flaptickler" being primordial examples. Besides, she also has a star-shaped mark on her right hand, which may be a small nod to Rockstar Games, further proving that IKZ only served as a big easter egg, which could explain why she was deleted in the first place.
Beta (FS):
Francis Sinclair's design was different in the beta; he sported a long coat, a half-buttoned shirt, and what appear to be a pair of boat shoes, but lacks any characteristic birthmark. His initial design could have been inspired by Back to the Future's Doc Brown, judging by these similarities.
Conclusion:
Rockstar Games probably changed the character's design to an Epsilon-themed one so they could still include a nod to the Epsilon Program seen in Grand Theft Auto: V. The Princess wasn't that important to the world of Red Dead, so Rockstar removed most of IKZ's presence in the game, reducing her entire story arc to a wanted poster on a wall and a few mentions.