I think the outcome will be the same but the way you get there will be different depending on which alignments you picked:
Sylvanas + N'Zoth's Gift:
Sylvanas gives the player character Xal'atath to crush the Rebel-Alliance coalition but the player character immediately turns on her and stabs her. "At the hour of her third death, she will usher in our coming".
Sylvanas without N'Zoth's Gift:
Sylvanas gives Nathanos Xal'atath to crush the Rebel-Alliance coalition but Nathanos has a change of heart and stabs her.
Alliance / Rebels + N'Zoth's Gift:
The player character kills Nathanos and takes Xal'atath from him before confronting Sylvanas and stabbing her with it.
Alliance / Rebels without N'Zoth's Gift:
Same as Sylvanas without N'Zoth's Gift scenario.
Either way Sylvanas will get stabbed (and survive / be forced to retreat) but the act will somehow usher in the return of the Black Empire, bringing the Alliance-Horde war to an end.