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.

Also also, if either of Amaznen or Acavna did willingly sacrifice themselves to meliorate the blow - why did They do that?  To briefly extend the lives of those mortals living upon one planet, until they came to Pharasma slightly later?  It's a strange trade for an ancient god to make, and Amaznen and Acavna are said to have been Lawful Neutral and Chaotic Neutral respectively; neither Good.

...Anything else?

Oh, all kinds of things, if dath ilan were to list out everything unusual whether or not the improbability is obviously relevant.  For example, it's said that Iomedae's helmet melted during Her ascension but remained intact enough to become a major artifact, the Thorncrown of Iomedae.  There's no artifacts like that said to be tied to Nethys's or Irori's ascension.  This doesn't obviously tie into any other anomalies, and doesn't seem intuitively shocking given the basic premise that the Starstone ascends things that get physically close to it, and dath ilan is not actually going anywhere with this observation; but if you're trying to actually think about a puzzle you will write everything like this down in one place.  If dath ilan forced itself to make up a guess about this random possibly anomalous fact - something something Starstone treats divinity in a way that makes spatial proximity matter to an unusual degree?

Any real scientific puzzle will contain a large number of extra pieces - and in advance of the solution, you don't know which pieces are extra.

So what does dath ilan think actually happened?

Lacking direct observation, you would probably have too many hypotheses and too little evidence to narrow them down.

You might speculate that the currently-known Starstone was the whole original 'poisonous remnant' rather than just a fragment.  If there were fragments, they might have been from pieces of moon, blown outward along a similar trajectory after the original Starstone blasted straight through the moon at high velocity.

You could theorize that the Starstone was aimed from the beginning to pierce through Golarion's moon toward Golarion - rather than Acavna moving the moon into place, and in futile error - and that the Starstone killed Acavna through Her connection to that moon.  Possibly Amaznen tried to save His sister-deity and the Starstone sucked the power out of Him and killed Him too.

This hardly seems certain.

Yes yes, it's admitted speculation; but it's often wise to start by trying to develop any consistent speculative model at all, if you're trained and confident in your own ability to throw out any pieces or wholes in which you later spot a problem.

Mmhm.  Well, keep speculating, then.

Maybe the alghollthus tried to catalyze the Starstone's 'poison' with their magic rather than having the power to create a weapon like that from scratch.

Or maybe, the alghollthus had nothing to do with the entire matter and were only blamed afterwards.

...Or maybe it wasn't the whole alghollthu civilization, but a particular band of alghollthu mages influenced by Rovagug, like how Rovagug is said to have infected a Sarenrite city built far above the Dead Vault.