It seems trying to match it up based on game dates doesn't really work and neither does the establishment of Atlus USA.
Again, might be some weird, possibly semantic details concerning acquisitions, renamings or something which was a period where they felt the "Atlus brand" wasn't present.
I guess all that matters is that they consider it's their 25th anniversary, but it'd be weird if they're just stating that because a lot of Atlus projects are to be released in 2014 and were like: "they'll never notice it's not actually our 25th anniversary."
Would have loved a logo.