Wasn't Vivec's flooding of Morrowind also how the Inner Sea was formed?
I think.
Dwemeri high priest Kagrenac then revealed that which he had built in the image of Vivec. It was a walking star, which burnt the armies of the Triune and destroyed the heartland of Veloth, creating the Inner Sea. - http://www.imperial-library.info/mwbooks/lessons.shtml
In my research of the very oldest Nord records, I found ancient maps which showed no island in the north of modern Morrowind -- just a region labeled "Dwemereth" which encompassed the island of Vvardenfell as we know it, as well as a rather wide swath of what is now the mainland. Indeed, as best as could be made out from the rather crude map, the coastline once extended some distance further north than Vvardenfell does now. - http://www.imperial-library.info/fsg/ghanburighanarticle1.shtml
So from this there was no Inner Sea in the Middle Merethic and it was formed around the same time as the Battle on Red Mountain.
However, Topal seems to have sailed it first in the Early Merethic:
Here is a man who follows his orders explicitly, and knows that he should have been going south-east through river ways to reach Firsthold. Looking at his maps, we can see that he attempted to find passages through, as he has mapped out the Inner Sea of Morrowind, and several of the swampy tributaries of Black Marsh, no doubt being turned away by the disease and fierce Argonian tribes that dissuaded many other explorers after him. - http://www.imperial-library.info/obbooks/father_niben.shtml
Which seems to be another one of Topals mysterious historical inconsistencies. The other one being sightings of Orcs in Highrock before there where Orcs any Orcs at all.
As such, I reckon that the original Poem of Father of the Niben doesn't actually come from the Merethic Era, but from a much later time period. It being a http://www.hbo.com/rome/.
edit:
The alternative is that Nordic cartographers svck, Vivec was being poetic without reason and the Inner Sea was formed at the impact of a heavenly body and has been there ever since. Though this isn't quite as interesting as a Anumidium induced landscaping.