Really interesting ideas in this thread!
My $0.02:
The thing I kept wondering when seeing the Mutilated was, why are they, all but one, mutilated?
- Maybe Shauriatas tortured them; or
- maybe they happened to lose body-parts in self-defense, the way Koringhus got his scars; or
- maybe they sacrificed a bunch of body parts for experiments with the Ark---maybe trying to get the Ark birth "Srâncyain"
All of these possibilities seem reasonable, but they don't answer the question of why just one of them isn't scarred. Here's one answer that works for all three possibilities: the unscarred one is Shauriatis, or was Shauriatis once.
Examine the scene where Kellhus talks to the Dûnsult. One of the first things he asks is "How long did it take to purge the Thousand Thousand Halls?":
"One thousand six-hundred and eleven days," the second figure replied. He alone appeared unscarred and intact, though his attitude was so remote as to be cruel.
"We could not cope with the Erratics," the third added. This one bore two great scars on his head:
the first a vaginal pit in lieu of his right eye; and the second more subtle, a slash the length of a hand-scythe, rimming the perimeter of his head from crown to throat, as if someone had abandoned an attempt to remove his face.
"That is," the Aspect-Emperor said, "until they took you captive."
(Note that the unscarred person rather un-Dûnyainishly has an expression that looks "cruel" to Malowebi.)
That last line seems like an intentional meaning to either Shauriatis or the Dûnyain: either "until [the Dûnyain] took [you, Shauriatis] captive" or "until [the Consult] took [you, the Dûnyain] captive". Throughout this whole conversation, the assumption seems to work: the unscarred one calls to and instructs Aurang; he never talks about Shauriatis in the third person---only the others do. He's the one who says "we have scrutinized the Ark." When the Dûnyain talk about their own history, the unscarred one does not contribute; instead he talks about the progenitors.
I think all of this is consistent with the idea that the Dûnyain merged souls and subsumed Shauriatis in some fashion; when they say "So Shauriatis alone was undone." what they mean is that they broke him down until he no longer had any individual identity.
[EDIT Madness: Fixed quote tag.]