This post contains spoilers for chapter 13 of Destructive Interference.
So. N. Looking forward to the comments to see if this made sense or not.
Quick summary of what was revealed in chapter 13: Ingo's Zorua siblings from Hisui were reincarnated as N and a Unovan Zoroark in modern times.
The in-universe explanation is basically just that sometimes Zorua spirits don't want to die and Ingo's Zorua brother and sister weren't done being part of Ingos story.
The real explanation is far longer.
Initially I was going to talk about this in Boss, Warden, Alpha (the unused but still posted epilogue where Ingo writes a memoir about the events of Masking) but I started writing Destructive Interference before I posted Boss, Warden, Alpha so this little detail was edited out:
Originally Ingo's Zorua brother was going to be a past incarnate of Emmet and Ingo's Zorua sister was going to be a past incarnate of Elesa.
Only two people have noticed this so far! I mostly edited it out of Masking but there are a few lines in the early chapters, especially chapter 1, that referenced this. The main thing that remained is that Ingo's sister/not-Elesa-anymore/Theta prefers to disguise herself as an Electric-type (Luxray) but there are a few other details intended to be foreshadowing were left in.
Note: Destructive Interference is a spin-off so Runt and Theta are not Emmet and Elesa or N in Masking. The timeline doesn't make sense for that.
To lay it out a little more clearly:
In Masking, Runt's ghost/soul (ghosts and souls are not the same thing in this fic but for convenience let's say they are) was taken from one of Lady Sneasler's kits. He goes to the modern world and was not further reincarnated. Ingo's sister's ghost/soul was taken from an Alpha Luxray. She remained in Hisui so it is still possible for her to be reincarnated as Elesa but I've never touched on this and don't plan to.
In Destructive Interference, Runt is a Sneasler kit turned Hisuian Zorua turned N. I never address if N is a Zoroark disguised as a human or not but it is implied that his past life as a Zorua is the reason he can understand Pokémon. Theta (Ingo's sister) was an Alpha Luxray turned Hisuian Zorua/Zoroark turned Unovan Zoroark. It is implied that N and Theta were reborn in modern Unova through "regular" means of reincarnation.
The original version of Masking had Ingo's Zorua siblings be "new" ghosts/souls. When they died in Hisui, they were reincarnated as Emmet and Elesa in modern Unova. I decided not to stick with this idea because I thought it was too complicated and would distract from my original intention with Masking (to explore how Zoroark illusions work but I gave up on that like halfway through and no one cared anyway).
I'm thinking about eventually doing another spin-off where I write out this idea of Emmet and Elesa as future lives of Runt and Theta but I don't want to commit to anything.
But back to Destructive Interference, it does seem kind of random that N and his Zoroark friend are Ingo's siblings and they're not in the fic for very long. This is intentional. Sometimes there are just regular people in stories that aren't main characters but affect the plot. Arceus just thought they deserved to know where their brother ended up and sent them to the future.
Runt and Theta totally could've been Emmet and Elesa in Destructive Interference but the appeal of the fic is waiting for Emmet's reaction when he learns Ingo is a Zoroark so if Emmet was also a Zoroark, I don't think it would be as satisfying.
TLDR; N and Theta are reincarnations of Ingo's Zorua siblings because they were always intended to be reincarnated.