Exactly, and thus they would know their race and gender, and that would render whatever nerevarine you played void.
That is probably exactly why it's kept so vague what actually happened to the Nerevarine after fulfilling all of Morrowind's quests. Bethesda writes the Nerevarine out in a vague manner so that players can decide for themselves what became of him or who he was.
6 years and no one knows where he/she is? That seems a little lazy on the devs part to me. The Nerevarine would be one of the most important people in the entire Empire political system. Someone who could unite all the various Dunmer Houses and Ashlander tribes would pose a serious threat to the Empires control of Vvardenfell. Maybe Uriel Septim had the Blades assassinate him.
Alternately, the Nerevarine could also be instrumental to eliminating Imperial opposition in Morrowind, since the Nerevarine, being as important as he is, would probably have a lot of influence, if the Nerevarine chooses to side with the Empire, it might do a lot to make the Dunmer at least more willing to tolerate it. And being an Outlander himself, the Nerevarine has little reason to want to remove the Imperial presence, and in fact would probably do everything within his power to ensure that foreign influences stay in Morrowind. And as Caius makes clear, the advantage of having a Nerevarine under its control are clearly present. Besides, if the Emperor had wanted to ensure that the Nerevarine could not unite the Duner against the Empire, he would probably see to it that the prisoner who has the appearance of fulfilling the Nerevarine prophecies can never fulfill them, not have that prisoner go and become the Nerevarine.
Vvardenfell is invaded by Daedra and, most likely, totally obliterated.
Ald-Rhun seemed to suffer that fate, and with it, the rest of Redoran as well, but as a whole, it doesn't sound like civilization on Vvardenfell has been destroyed to me. In fact, Hlaalu at least seems to be doing pretty well, and I'd think that losing their holdings on Vvardenfell would have been a pretty hard blow.