I’m not sure where the “bullshit history that turned out to be true” is here. Was the eruption of Thera c. 1600 BC really considered a myth at one time? That’s not my understanding, but I’m not a subject matter expert, so I could very well be wrong.
As to the Thera = Atlantis hypothesis, it really doesn’t hold any water, if you’ll excuse the pun. Thera had a Minoan colony at Akrotiri that was obliterated by the eruption, but the Minoan “mainland” on Crete survived. As I understand it, there’s conflicting opinion among archaeologists and historians as to the extent of the damage inflicted on Minoan Crete and the impact on Minoan civilization. Minoan artifacts have been found above the ash layer from the eruption, from centuries later. It was around that time that archaeological evidence starts turning up of the Myceneans displacing, conquering, or absorbing the Minoans, so it seems quite plausible it was a significant, even precipitating, factor in Minoan Crete’s long-term decline, but it was hardly the destruction of a great island-continent and its empire in a single day and night.
Then there’s the problem that Minoan Crete only resembles Plato’s Atlantis if you tilt your head just right, squint really hard, and engage in liberal hand-waving.
And there’s the not exactly trivial problem that Plato explicitly places Atlantis “beyond the Pillars of Hercules”, which we know from copious contemporaneous evidence refers to the Straits of Gibralter - Plato’s Atlantis was in the Atlantic Ocean, not the Eastern Mediterranean. Plato also claims that the remnants of sunken Atlantis are still present as muddy shoals that make navigation difficult and dangerous. Not many Athenians of Plato’s day would have had any first hand, or even second-hand, knowledge of the Atlantic, so that detail probably wouldn’t have seemed implausible. On the other hand, the Athenians of Plato’s day had extensive first-hand experience with the Eastern Mediterranean, and its distinct lack of “muddy shoals”.
You can find some hand-waving among “Thera = Atlantis” supporters that the phrase “the Pillars of Hercules” was also used to describe some geographical feature of the Easter Mediterranean, but that supposed alternate use is otherwise completely unattested, and strikes me as pretty blatant special pleading.
You’ll also find claims that Plato took the basic facts of the Thera eruption and transplanted them to the Atlantic for story reasons. Which, ok, but then, to what extent is Thera even really Atlantis anymore? Plato almost certainly drew upon any number of folk-historical memories of past subsidences, catastrophic floods, volcanic eruptions, and other disasters, as well as folk-historical memories of the Minoans, Mycenaeans, and other foreign empires, as inspiration, and to lend some verisimilitude to his fable.
But I don’t think modern evidence of Thera’s eruption has had the effect of revealing any “bullshit history that turned out to be true.”