While I haven't managed to get my hands on a translated copy of If..., the (absolutly horrible) sequel manga & the Megami Tensei wiki describe it as a side-story, taking place in the universe of SMT I & II. Characters from SMTI are encountered and such, and the nuclear holocaust was right on track to happen as of when I gave up on the manga.
While there is a character from If... in the Persona games, I saw that as the same as the way Kei Nanjou has a presence in Persona 3 even though it's not in the same universe(s) as the previous Persona games. They do have a tendency to do tributes, like the Demifiend in Digital Devil Saga and Alice in several games. While Persona 3 doesn't justify her either, the Devil Summoner games kind of do, but in those it's fairly easy to too easy to access alternate timelines.
Although that's getting off-topic...
Re. Yamaoka, I'll see if anybody says anything when I get there this playthrough that will clear it up, but, I'm fairly sure there was another occassion of ghosts being used as Personae. I can't seem to find a reference for it at the moment, however, so I can't be sure they were ghost-ghosts as opposed to what Nocturne did that time...
In the interests of staying on topic, let me restate my points:
1. Aizen-with-glasses was a mask/persona of Aizen's that could have inspired Aizen Myouou,
2. ...and is thus equivalent to Maskados et al. since:
3. Persona do not come from the individual's subconscious, but the collective unconscious.
4. Aizen-without-glasses is still a persona, as all aspects of human personalities are personae. However, he'd be a different persona from Aizen Myouou.
5. Aizen, as a shinigami, is a spirit that can be embodied in vessels, and thus would likely be easier to summon than a normal non-consenting persona. (I'd put 'real human core personality' here, except there's no such thing.)
6. It is possible to get personalities that were once part of a 'human aggregate' from the sea of souls/collective unconscious: Maskados, Yamaoka, etc. (I'm aware you disagree with this.)
7. Fusion accidents happen.
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Given the above, I think a crossover fic with this premise is very doable. You seem to disagree, but a lot of it seems to be coming down to a matter of opinion, for instance was Yamaoka real or imaginary? That's especially difficult in the Persona universe, as we're all 'imaginary' by those standards, existing in what we show to ourselves and the world and the memories that leaves behind, which was the reason them remembering in P2:EP would have destroyed the current 'universe.'
The answer to 'is he Kei's memory or is he Yamaoka' could very well be both. Since Kei's memory would = the Yamaoka persona/mask and since that mask would be part of the sea of unconscious and that's what it's summoned from.
Of course, there's a lot of disagreement among fic writers on the Persona laws of physics. There was this one fic that Stud Minato a bit but it was tolerable, but at one point this character said they'd killed Philemon and I was all...
Because first off, they'd essentially killed him for not being able to screw the laws of physics to hand him everything he'd wanted on a silver platter instead of only 90%, he was the one that ruined it, and did he want Philemon to screw with people the way Narlathotep did?
Instead he basically handed the characters the tools to solve their own problems, and how is it bad to be treated like a freaking responsible adult? The character was basically whining about not being babied, like Philemon had been uncaring instead of demonstrating that he respected him by leaving it in his hands. (Undeserved respect, in the case of this version...)
Not to mention that the main 'verse of the fic was P3, that pointed out that Nyx and other entities on that level were pretty unkillable. You wouldn't kill Philemon with a sword, you'd kill him by going around and convincing every single person in the world that they were completly worthless and should lie down and die, given what Philemon embodies. And since people (like the fic's Minato) still seemed to have healthy egos, believed they deserved to exist and were trying to control their own destinies and make them better, Philemon would still have to be alive.
(Frankly, I wish they'd kept Philemon around. And Nyarlathotep, because seriously. A Lovecraftian cosmic horror as the final boss! How cool is that?)
I should probably just write my own crossover, except for some reason I just don't want to write Aizen. He can be an interesting character to read, but he hits a couple of my pet peeves, or maybe it's how the manga's done that does this, and I can't seem to care enough to get an Aizen muse.