Even if these islands near Gibralter existed, they would have been insignificant specks of land, hardly an impressive civilization. Their eventual disappearance in a rising sea would have been no more impressive than what happened to any coastal city of the time and probably less so.
Thira, on the other hand, was the at the center of the Minoan Civilization, perhaps the most advanced and impressive one on the planet at the time. It was blown to bits and disappeared into the sea with only fragments of the volcano making up some of the beautiful Greek isles today.
Legends sometimes get it wrong.
I once thought that too. I don't think the explosion of Thera (1628BC) is old enough. If Atlantis existed in more recent times there would have been more evidence and more written about it. The scarity of information about Atlantis hints at an ancient date. IMO (In the 1300's a Jewish guy named Nazi (no kidding) owned the island of Thera)