Out of all the stuff the "Saxons" blatantly ignored so they could rewrite the history of northern Dwilight the way they wanted it to be, the claim that they were the best sailors ever is what bothered you? Besides, maybe they /were/ better than the Madinans. Madinans have no special dispensation that would make them the best sailors the world has ever seen.
IMNSHO, claims such as "best X ever" are pretty qualitative, and subject to individual judgment. So long as it's an IC claim, then they can claim whatever they want. It's natural for different people to have different opinions. Now, if the players start OOC arguing "this fictional civilization I just invented were better at something than the fictional civilization you just created", then, yeah, that's lame.
Aside from that, have fun with the project. It's a lot of work, but it should be pretty interesting.
Everybody knows that D'Harans are the best sailors ever. Madinans stick to the land 99% of the time.
That being said, pre-history is a pretty darn long time. Cultures evolve and replace themselves. Just as the Toltecs came in first and the Aztecs came in after, there's no contradiction in saying that "X were here in the past" while saying "Y was here in the past", as "past" is vague.
