What I tried saying was that the concept of dragonborn wasn't created by then... So the devs had no way of intending the Nerevarine to be the same kind of Dragonborn as the one in Skyrim is...
So that does mean that the Nerevarine Dragon-born part meant being born in the Empire, which is kind off special as Morrowind had never been ruled by a party outside of Morrowind, ever.
I don't think it's that simple. Morrowind was part of the Empire at the time, meaning anyone born in Morrowind was also born in the Empire.
Dragon-born has something to do with the Septims, who are all said to have dragon blood. In Sermon 9 of the 36 Lessons of Vivec, Ysmir, Dragon of the North (otherwise known as Talos, or Tiber Septim), is depicted as having the ability to use Thu'um, although none of his future generations are said to have had the same power. That would imply that all the Septims were Dragonborn, but couldn't learn Thu'um because dragons no longer existed (meaning they could absord the souls of dragons, but had no souls to absorb and therefore couldn't learn Thu'um).
So yes, the concept of Dragonborn did exist at the time. It just wasn't as refined or apparent as it is in Skyrim.