"The Abnormality previously identified by X as a significant threat has recently been spotted moving towards Kamihama City. I will be allocating all my available resources towards tracking it."
Just to remind people. Kamihama is where currently:
She had aimed for Kamihama City, close enough to the center of the Migration to catch the torrent of Witches but out of the way enough to avoid conflict. Her Magic had reassured her with previews and visions; all showing the City as a simple and uneventful place. And so she had appeared there in a hidden back-alley, ready for a few short hunts.
The Adult Who Tells Lies resides.
So let us not forget that TWO Alephs are about to meet up soon-ish.
---
But in regards about "The Truth of Soul Gems".
This could just be an AU thing for this story (and I'd approve if it is), but Lobotomy - which modifies the "self":
A web of branching streams of Light spring from Homura's sleeping form. It twists and sways as if responding to some nonexistent wind, fading in and out of sight at seemingly random points.
You reach out, and Light streams from Mami's body in glimmering branches that fill the room.
Brings the tree of their "self" out of their
Bodies and not their Soul Gems.
So at least in this story X's skepticism in regards to Soul Gems actually being the Person's Soul has at least some valid justification.
You ease into the comparison between Soul Gems and Souls. Partly because you know how well to expect that reveal to go over, partly because having established some facts already should make the reveal go over easier when it happens, and partly because you don't completely buy the whole "soul" business to begin with. Kyubey's definitely manipulated something deeply related to a person's self, but if you had a nickel for every person who claimed they could tell you what a soul is you'd have had enough money to stop running the Corporation as an actual business along with a lot of answers that didn't match up.
So putting Soul Gems as deeply related and the now most vital organ of a Magical Girl, but not actually the Magical Girl herself may be a valid option with this supporting evidence.
---
And at least for the Witch reveal: X
can just be very gentle with the wording.
Especially with the doubt cast on how much the Soul Gem actually makes up the MG in this story.
Kyubey is currently occupied and so can't twist the knife. So we should use this opportunity to inform how the kids think about the topic.
Even if only in a "This
could happen and is not the only or most natural way for this to go" way.
Doesn't have to be 100% true, just needs to be digestible enough that the kids don't immediately break down.
And give them resistance for when Kyubey tries to tell them the "You are made to turn into monsters and fuel the universe" spiel.
Let's not forget, in this story Kyubey:
Are Witches really Magical Girls, or are they just sort of a byproduct?"
"I don't actually know the answer to that. The specifics of Witches and their humanity was never important to gathering energy, so it wasn't investigated beyond the surface level. Some Magical Girls have tried in the past, but nothing ever came of their research. Besides, the individual identities of humans are too complex and driven by illogical impulses to fully understand."
Doesn't actually know for certain.
And thus having X ease the kids that Witchdom is just a disease that X may very well be able to cure even soon-ish
should help a lot with dealing with it.
Also in canon Kyoko is one of those who deal with the Witchbomb terribly (AFAIR from PMAS discussions on the topic).
So
whatever let her deal with it well here, may very well help convince Mami that not all is lost.
If it was good enough to give Kyoko peace, it should well allow her - in turn - to help ease Mami.
And as these last two sentences read a bit oddly, but I am not made of Time TLDR:
Kyoko usually deals badly with the Witchbomb, now she doesn't.
She will be here for that if the reveal happens and so can Friendship-speech at Mami to help us.
We have X, Yuma and a weirdly well-adjusted Kyoko here to give emotional aid.
And the Homura Timestop + Aleph Lobotomy Panic buttons.
As long as Homura is away enough from Mami to activate the shield before getting tagged by a Ribbon even many of the worse case scenarios should be handleable.
But I am also one who would never be comfortable with the Witch Reveal, so I do not think I have much more to add here.