It's a possible explanation for the people, but the similarities in geography have a much simpler explanation: 12,000 years is a huge amount of time for people, but not that much on a geological timescale.
Wikipedia tells me that the Earth's continents were "essentially at their present positions" during the
Pleistocene Era, spanning from 2.5 million years ago to 11,700 years ago. So Hydaelyn's continents would likewise be in their modern configuration pre-Sundering and each version will have had similar large-scale influences over time.