So, after a couple of re reads, I must say I enjoy the fic immensely.
I was honestly worried when the topic of rape popped up, considering most works of literature handle that issue with all the subtlety and understanding of a pneumatic drill hammer on an echo chamber (they don't handle it well is what I am saying).
Matthew hits the very difficult balance of "asshole" and "desperately wants to connect to other people, but can't really connect because Magi are god awful people and Beryl fucked him something fierce and then Marisbilly drop kicked those issues and made them worse. ".
The alternate singularities are awesome and are praise worthy LaVoisin was someone I had to look up and fit to a T to the kind of insane horror you wanted to convey an you did it well.
Minor problem here, Marie and Co felt like they had too little screen time, even in the Halloween event, for some of the most important figures of french history they felt overshadowed by Charlie and the Apoc Gang.
I personally would go back at some point and perhaps write in a chapter or two from their PoV, because Marie, D'eon and Mozart felt like they should had a bigger spotlight, more so considering we have Sanson as an enemy.
The characterization is well done and I honestly like Ritsuka as a character, as well not Shirou and the pics, specially the naked ape bit after gilgamesh went AUO on the cast and well it comes out as the right kind of Papa Wolf trope, not overbearing, but also paying enough attention to help his kids if the situation is out of his hands.
Speaking of Shirou... I have a couple of quibbles with your characterization of him during the FGO x FSN arc, mostly centered about "but she's a girl."
The original Japanese VN (I believe mirrormoon took this out by accident... along a chunk of the plot and information), whenever the situation is Saber Combat Death Killing, or anything that involves something close to that combination Shirou has a PTSD flashback to Saber bleeding out, only standing up with her sword and her looking in immense pain. Like "OH GOD MAKE IT STOP" tiers of pain. However, Shirou is not a master wordsmith and thus can't generate an entire speech on the spot that explains he feels its wrong to make Saber fight because he can't stand the thought of her dying or at least, or being injured so terribly... because it triggers his other PTSD.
So, yeah, its not that Shirou is against women fighting, is specifically Saber due to the circumstances I just described, he wouldn't have any problem letting Musashi duke it out if she wanted to.
This is a problem also created by the DEEN anime that refused to show this rather important piece of info, so instead of a nuanced thought on the trauma that has begun to pile on poor Shirou... he comes as sexist at best, misogynistic at worst.
As for how i would improve it, I'd honestly take that scene out, given its nature derived of false representations, that's my suggestion, take it out and edit the chapters around the arc to accommodate.
I am also a bit iffy on the whole "Merlin and Morgan decided to accelerate Shirou and EMIYA's memory synchronization to speed things up". It feels somewhat like it was done to please Matthew and keep him from trying to murder Shirou (which at that point had become in my opinion, a moot point, as the Dream Cycle had shown Matt how Shirou was and became what he is via the fire. Which put things in context), and I have mixed feelings on it:
On one hand, its good because it avoids the UBW drama of EMIYA hating his past self.
On the other hand I feel its bad because it avoids the UBW drama of EMIYA hating his past self. Even if previously you had mentioned he's made peace, this could've been a golden opportunity to explore things a bit more in depth for EMIYA, has he truly made peace with his choices? Or is this yet another facet of his madness? (A thing mirrormoon butchered, EMIYA quite readily admits he's bugfuck nuts, the "My core is twisted in madness" is not Caladbolg's II trigger, but rather its EMIYA musing to himself the sad reality he's crazy).
Its one of those odd bumps in the fic, and thus, I come back to the mixed feelings.
I would honestly rewrite it a bit, perhaps even have EMIYA and Shirou discuss their points, in the VN EMIYA is desperate, he's sure he won't achieve anything if he kills Shirou, but on the other hand, he's still thinking that he needs to get out somehow, because the experience has broken him.
Everything else is perfect, Matthew doubly dunking on BB is just perfect, I had to put a pillow over my head since it was 3AM when I hit that section for the first time and I wouldn't stop laughing my ass off. Really, BB getting dunked is one of the few things in life that cannot be supplanted. Good against avenger she might be, it doesn't means she's not lacking, severely in the WIS stat... as shown in the manga with Kazuradrop.
Honestly I hope to see more of this work because its genuinely difficult to find good Fate material to read, with most being barely passable.
Those are my two cents, hope you like 'em!