I could be wrong, but I believe the logic goes that if the entire area was land, the cities in the area were allied with each other and this allowed for the sharing of technology between them. When the sea rushed in, it destroyed all but the few cities left at the edge of the new sea, leaving us with the "mystery" of how these few cities connected by only the sea could all have independently developed this tech, when no one else did.
I read an interesting paper about 10 or 15 years ago positing that during the last ice age the levels of the oceans were reduced to the point that the Mediterranean Sea was either much smaller or non existent. Unfortunately the people at that time didn't get the warning about climate change coming.. as the global ice caps shrunk back to "normal" levels, the Mediterranean was formed. (In reality, this was aprox 20k years ago, not the 10 to 12k spoken of in regards to Atlantis.)
I don't really follow Atlantis stuff much, but there has been at least some scientific research along the lines of what H.G. Wells was making up; Whether that theory has been confirmed or tossed out I really have no idea, but I wouldn't say that "scientific theories" don't cover this.
Stellar rays prove fibbing never pays. Embezzlement is another matter.