Writeup/Musings on the Dark Prognosticus's Origins:
The long and short of it is, we have no idea where the thing came from. So anyway, here's my idea. We can probably safely say that it was written by somebody, since that's what anybody to ever comment on its origins assumes, even those we aren't given reason to suspect might be wrong (like Merlumina and Garson), and thus it probably isn't a primordial artifact of doom from the dawn of time or anything like that. I do have one sort of personal headcanon/pet theory on it, though. First, we have to turn to the Light Prognosticus, and how it was made. Shamans across the Paper Mario series (and beyond it, as with Madame Clairvoya) demonstrate the ability to look into the future, using/calling on the power of the Stars to do so.
Stars are also heavily linked in concept across the entire Mario series to the notion of fate. Rosalina, for example, talks about how the will to be reunited with one you love is a force more powerful than fate, beyond the whims of the Stars. This is most likely why they can be read and used in order to look into the future. The Light Prognosticus is said to have been written by Merlumina and Merloo, who similarly had the ability to look into the future. And, given that there's a star right on the cover of it, it stands to reason that this is most likely how the Light Prognosticus was written as well.
So then we have to get into what kind of fate exactly the Stars are responsible for. The universe is born time and time again, and each cycle is very similar to the last, but we are told that it never unfolds in quite the same way. Fate is spoken of rather insistently as a thing that can be broken, can be defied, that it is our will and our care, for ourselves and for each other, that can do so. Fortunetellers and seers give advice, not on what the cosmos has already written you shall do, but on what you should do, what you can do, what can bring about the sort of future you desire.
Similarly, there is a distinction that Merlon makes between the Light and Dark Prognosticus. He says, the Light Prognosticus was written in response to the Dark one, created to counteract it, and as such isn't "truly prophetic". Now, it was explicitly made with future vision, and is very much a prophecy even down to its name, so it's safe to assume that he means something different here. What I think he refers to is what I will term the comparative "force" of the two prophecies.
The Light Prognosticus emphasizes choice at any place it can, champions possibility within the constraints of fate, it is a document written with the hope that the Dark Prognosticus's fated outcome could be overturned. Its words ring across the story with a word the Dark Prognosticus fails to utter - "if". The LP acknowledges with humility that its predictions are merely one possibility, but that it is the path with the best chance to overcome the Dark Prognosticus.
The Dark Prognosticus, by contrast, admits no such thing. As far as the prophecy of destruction is concerned, its word is absolute, inerrant. And it backs this up! In more than 3000 years of its history, this little black book has brought ruin to nations in wars fought over its possession, all with information it predicted from the beginning. Until the very end, its every word comes to pass, and it's only at the events of its final page that the Purity Heart's power contradicts and defeats it. The Light Prognosticus had to work within its gaps. On nearly every event that will happen, the two books are essentially in agreement. The Light Prognosticus operates by describing the path of the heroes and the Pure Hearts, the power of love that they believed could overcome the prophecy directly, outside of what the Dark Prognosticus's words specify.
Now I'll circle back the Stars, and that which they exist in opposition to. The nature of the Stars, seen as a constant across the Mario series, is to give, to sacrifice. They are the granters of wishes, the progenitors of life, the essence from which the cosmos itself is woven. The Power of the Stars is no less than the lifeblood of the universe itself, and the Stars give themselves up to these causes knowing this. This is reflected in the kind of fate they are linked to. The space of potential, the navigation of the endless futures that there might be. But what, then, is their antithesis? We see it in the Ztars.
Where the Stars radiate light and hope, the Ztars are bitter icons of darkness and regret. Where the Stars so universally lend their power, the Dark Star spends the entirety of its game feverishly hunting down the power that was taken from it, insisting not only on making itself whole, but consuming all the world in darkness. And that is, I think, what darkness is in Mario's context. Selfishness at the expense of another. The Shroobs, whose corruption of Peach's Castle includes Ztar-like imagery, and who act in a similar way to the Ztars as dark mirrors of the Mario world we know, are exemplars of this selfishness, living parasitically off of the destruction and consumption of anything else, draining the life from worlds after they have made their own a husk.
I think the conflict of the Light and Dark Prognosticus is a similar one, a conflict of opposing forms of fate, the potential and the absolute, the giving and the selfish. The Dark Prognosticus insists upon itself, constricts the space of potential toward its ends, ultimately its aim is to destroy everything, in the ontologically most selfish possible act. This, I think makes it strongly connected in spirit to the broader Mario series' conception of darkness and evil. And it is for this reason that I think, if the Dark Prognosticus is to have any origin at all, that origin lies in the Ztars.