I always thought that while they have made an effort to tie these side spin off stuff into the overall world/main story, they still functioned like a spin off Omake. Like even Person Q, makes it so all of it takes place in a way that works within THAT time period.
I don't think I would like main series tittles continuing that directly w/ repeat characters being heavily in the plot. I would be okay with little tie ins etc. But I hope they leave the spin off stuff as it is. I mean, it works for what it is (how they integrated it all together). And that's great. But eh.
BTW I love love love your avatar. I love that game/character so much.