What does "the distinction is ultimately semantic" mean?

The world would perhaps not be made literally unrecognizable by that flooding, but the distinction is ultimately semantic.

The world would perhaps not be caused to be "unrecognizable" [in the primary meaning of "recognizable", i.e. "incapable of being recognized as the planet Earth"] by that flooding, but the distinction [between being "recognizable or not"] is ultimately one that is found in what the speaker/writer means by "unrecognizable".

The writer is implying that although Earth itself would still be recognised as the planet Earth, (i.e. literally "recognised") everything on earth would have been changed such that the land would not be recognised (i.e. in a more restricted sense) by a person who had seen it before the flood.