We have to keep in mind that we actually know that Allag existed before it was an Empire. Their knowledge of summoning came from before those times, way before their aetherochemical revolution, when they were menaced by people who invoked eikons.
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I think you might be misremembering. Allag started with Xande as an empire and the first thing he did was to collect mages for his army to conquer Eorzea.
"Xande used his uncanny intelligence and charisma to build a nation that, while founded in science, did not deny the magic of the Second Astral Era."
"In less than a year, Allag was the largest nation in Eorzea and Xande crowned himself emperor."
Allag wasn't the victim being menaced by people with eikons, they were the ones menacing people who had eikons. And according to the EE, Aetherochemistry was a thing during Xande's time at the very beginning of the Allagan Empire. It's just that everything we're used to seeing of it is from the Late Allagan, during Amon's time. Amon was from 1000 years after Xande but it was an aetherochemical empire from the very beginning. The Third Astral Era was founded on science and eschewed magic, but it was Xande who brought magic and science together.
This is a bit of an interesting passage, becuase if we take it literally then it's... sort of impossible? Like, you can't just come out the gate and found an empire day one; typically, a nation of another type becomes an empire, usually by conquering other nations. For some in-game-rooted examples, the Roman Empire has an origin pretty close to Garlemald, where a republic became an empire under one guy deciding to do things differently. The Mongol Empire started when the guy we know as Genghis Khan was elected leader of a bunch of different tribes, which you could potentially read as similar to Gulool Ja Ja (but I would argue probably isn't an especially accurate reading of either figure).
Put simply: there's no way that we aren't missing details here, because the founding of empires just don't work the way that the EE1 describes Allag's origins. What those details are, I couldn't tell you. My honest best guess is that Allag maybe started similar to the Mongols, as a pile of disparate tribes unified under one banner, but that's based on a reading of one sentence in the EE1.
It was just the largest nation in eorzea, and you don’t really need an enormous empire to declare yourself emperor for pr purposes. Maybe a cabin just outside your established territory to make sure no one’s going to argue about technicalities. Not like anyone would really complain, the calamity of fire sounded pretty thorough and unpleasant. It wouldn’t really have to be that much bigger than rowena’s current empire, which may be deliberately mimicking allag - base by the crystal tower, further expansion into the ruins of a now-gone civilisation, having adventurers bringing Allagan information storage units in their thousands etc.
I don’t really see any reason to dismiss it out of hand unless there’s some extra lore added. Not like the player hasn’t effected rapid and drastic change, and that’s without any help from the empire builder hobbyist.
It's more than just one sentence in EE1.
You need to remember the context in which Xande began his empire. After the Second Umbral Era, magic was taboo. Xande collected the descendants of priests and witches from the Second Astral Era and formed a powerful mage corps. None of his enemies had magic or at least anything close to the extent that he did. It's like bringing bombs to a battlefield where everyone else is hitting each other with sticks. In that context, it's very easy to create a powerbase and the conquer everyone else around you and form an empire in 1 year, exactly as the book describes.
The Allagans also had Ascians scripting the entire creation of the Allagan Empire, which certainly helped as well. Xande very well likely had Emet-Selch's help orchestrating the opening act from what the man himself had described. He even said that Garlemald paled in comparison to Allag. The Garleans have no magic, nor even the capacity to wield it. They were only able to fight on equal footing with guns, contracts with voidsent, and Roegadyn battle mage mercenaries. It wasn't until Emet-Selch that magitek took off and they were able to make an empire.
Now think of a world that had just forsaken magic because of its role in the previous umbral era and 1 guy gathers together all the outcast mages. With the power of magic while everyone else has none, there wasn't much in his way and Allag was able to conquer much faster and more efficiently than anything in our world or even the Garleans. Plus, Emet-Selch probably uplifted the magical understanding of early Allag just like he uplifted the science of Garlemald.
What I took was straight from Eorzea Encyclopedia. But just because they were using tomestones at the end of the Allagan Empire doesn't mean they weren't using books a thousand years previously when Xande initially started conquering everything and rebels with eikons were opposing them.
Besides, the section of Allag regarding Aetherochemistry says that the first bits of it were siege weapons and cranes. They had to start somewhere and didn't make airships and computers directly after bashing two rocks against each other. But the empire was founded upon that early combination of magic and machine and it continued ever since.