There could have been another change in coastlines after the Thera eruption. That must have caused huge tsunamis. Northern Crete would have been right in their path.
Athens is on the Eastern coast of Greece and could well have been affected too.
But one would suppose that a large tsunami would wash out a land bridge, not create one, unless it piled up the sea bed in shallow water.

Have any studies been made of possible coastline alterations at that time?

He was intelligent. His people were literate so at least some data about observed changes in his environment could be based on those limited records plus he could have asked the locals about what their traditions said about local changes. He goes to a land mass with a name suggesting it was an island. He can see a narrow neck of lowland/ marsh with little relief between the former island and the mainland. He’s pretty much going to know that such locations are sediment traps and that before that marsh/lowland was filled with sediment the place would have been an island.

Learning some things requires high tech, detailed histories of long ago events, and modern day science. Figuring out others requires little more than a working brain and observation plus perhaps a few old storeis and limited written records and this is clearly in the last camp. Once you understand the location is a sediment trap all you have to do is mentally remove the sediment to understand what the location was like in the past.