The part that isn't real is, in its own way, very straightforward; and the mask over it is being done correctly, such that the only way to guess it would be on pure priors.

If you looked at that complicated situation developing around Cheliax and trusted your lying eyes, you would get the impression that Carissa Sevar was playing a close and clever and complicated game, concealing her real intentions from at least your side and possibly all the sides, setting in motion some very long-term strategies - strategies spanning a timescale of months, maybe even years.

You would think you had that much time to think, that much time to plan.

Anyone who made that mistake and took their leisure would have no chance to act at all before the endgame began.

And then, it begins.

Turn now to regard the city of Absalom (in this age called also the City of Lost Omens), on the southeast coast of the Isle of Kortos, where the Starstone was raised up from the sea and closed up in the impenetrable magical fortress of the Starstone Cathedral...

Of which it is said that the alghollthus called down a poisonous remnant of an unborn world, meant to strike upon the rival human civilization of Azlant; the ancient moon-goddess Acavna moved Golarion's moon into position to intercept the missile; but instead the missile shattered into thousands of pieces while continuing toward Golarion; and the missile's fragments pierced Acavna and killed Her; and then Her brother Amaznen, god of knowledge and magic, sacrificed Himself to neutralize the alghollthu magic upon those fragments and prevent them from destroying all Golarion; and the fragment now called Starstone fell into the sea; and eventually Aroden found that fragment, and it turned Him and several other people into gods.

Ah, Golarion?

Yes, dath ilan?

There are elements of this story that make less than total sense to someone isekaied in from a physicalist civilization, trying to visualize out the entire process, step by step...

Actually, no.  That's understating the case.

If something that strange was written in dath ilan, it would be inside a children's-book; and you would realize that the real answer was meant to be sought out by young adults, when you were old enough to notice Problems with what had been claimed by the children's-book in your bedroom.

(The children's-books of dath ilan are not visibly author-signed, and never attested-to by any specific grownup, nor gifted to you by specific adults; they're just there in your bedroom, when you grow up.  And if you ask your parents they'll truthfully tell you that they didn't put the books there.  And your parents never speak to you of anything that you read in a children's-book; for those are children's books, and only children speak of them to each other.

As the saying goes in dath ilan, trying to raise a child on only true books is like trying to train a statistical classifier on only positive examples!

And furthermore - as is so obvious as to hardly need stating after the original proverb - having all the true books be written in a nonfiction voice, while all the untrue books are written in a fiction voice, would be introducing an oversimplified hyperplanar separator that would prevent a simple statistical algorithm from learning subtler features.)

...That's not how things are done in Golarion.

Indeed.  But someone who did grow up in dath ilan sure will notice when the Starstone book story sounds very very odd.

So what's wrong with the standard story?

...It's hard to decide where to start, but one has to start somewhere, so:

Start with the notion that the "remnant of an unborn world", having shattered upon contact with Golarion's moon, which a god had moved into position for interception, was not thereby successfully deflected.

Things that hit a moon hard and break into fragments don't usually stay on the same trajectory after that, narrowly enough to hit a planet.  The width of Golarion in its moon's sky is only 0.01% of that sky's angular area.  You cannot randomly hit a planet, starting from a moon, if the course is at all perturbed.  This story requires the Starstone to be strong enough to blow through the moon, trajectory unperturbed, while shattering into a thousand pieces along the way.

One would also normally think a space missile could be deflected more easily than by moving a moon to intercept it, even if some goddess has an especially easy time moving around moons.  If a ballistic space-missile is coming from far enough away that you have time to move a moon into place for interception, at any reasonable speed a moon should attain, you could apply a much lighter deflection earlier in that missile's trajectory.

Isekai protagonists from science-worlds likewise know what happens when planets fail to be born.  You end up with asteroids.  They aren't especially poisonous.

Then there's the notion that Acavna waited around in place near the missile collision site, or missile exit site, to be hit by fragments large enough or fast enough to kill a goddess, which She didn't see coming and dodge.  Again as science protagonists know, when you are dealing with moving moons around, and distances on the scale of planets, it is really hard for anything to hit anything by accident.

Possibly there was an original missile approaching at near-lightspeed; and when it collided with the moon, that sprayed up so many massive fragments that 0.01% of them hitting Golarion would still have ended life on the surface...

But that doesn't square with Amaznen needing to sacrifice Himself to neutralize magic on those fragments.  If secondary ejecta had been the primary threat to Golarion, they'd have been an unmagical threat.

You'd furthermore think that the alghollthus, if they were able to steer such a hypothetical hyperkinetic missile at all, would have known a missile at that energy would utterly destroy Golarion's crust including themselves if not intercepted.

Also if the alghollthu magic upon the fragments was potent enough to lay Golarion waste in its own right, apart from the fragments' kinetic energy, and required Amaznen's self-sacrifice to neutralize - then why should the alghollthus not lay that lethal magic directly about Azlant?  Why put it on a distant incoming asteroid first?

And furthermore - though this is not a physicalist area of expertise, it comes up if you just visualize out events and think about them - supposedly Acavna's divinity stuck to those fragments that killed Her, one of which was the Starstone, which then reached Golarion and became individually able to create gods on the order of Aroden.

Aroden was the strongest of mortal-ascended gods.  Hitting Acavna should not create thousands of fragments all of which could then create Arodens.

Arguendo:  Possibly all of Acavna's divinity stuck to the Starstone and not to any other fragments that killed Her?  Maybe it was that exact fragment that struck the final blow?

Counterarguendo:  Maybe, but then that's another weight of burdensome improbability required to make the whole story work.  One also notes, as an isekai protagonist reading through other stories of gods' deaths, that it is not usually said that the weapon that kills them retains their divinity.