Crete, which was destroyed by a volcanic eruption:

https://en.wikipedia.org/wiki/Minoan_eruption

Or Santorini https://en.wikipedia.org/wiki/Santorini#Speculation_on_an_At...

Yeah, both were part of the Minoan civilization, which suffered significant decline after the eruption.

Do you also wonder what inspired J K Rowling's Harry Potter? Or Ayn Rand's Atlas Shrugged?

We are quite capable of pure fiction with symbolic inspirations, there is no need to suspect "a kernel of truth" behind any speculation.

Many classical mythologies had basis in reality: the Iliad is a great example. Why are we so sure Atlantis is a myth (or allegory) while the stories of the Bible are based on real events? It’s just not that simple.

That's very simple: because Atlantis was presented as an allegory by its inventor, while most of the Bible was intended as history. Wondering where the real Atlantis was makes about as much sense as asking who was the historical prodigal son...

We know Europe is a real place and that actual countries called France and the UK existed at the time HP is set in.