In a small bowl, combine the sugar and flour and set aside. Using an electric hand mixer or stand mixer fitted with the paddle attachment, beat the cream cheese on medium speed until smooth. With the mixer running, slowly pour in the sugar/flour mixture and beat until incorporated. Stop the mixer occasionally to scrape down the sides of the bowl and the paddle as needed.
With the mixer on low, add in the vanilla, nutmeg, cinnamon and salt and then slowly pour in the eggnog; mix until just combined. Add the egg yolk, then the whole eggs one at a time, allowing each egg to incorporate completely before adding in the next. Stop the mixer occasionally to scrape down the sides of the bowl and the paddle as needed.
Pour the filling into the prepared crust, tap to remove any bubbles, and bake until the edges of the cheesecake are browned and the center is barely set, for about 60 minutes. Turn OFF the oven and leave the cheesecake in the oven for 1 hour.
Remove the cheesecake from the oven and place on a cooling rack. Once cooled, you can make the chocolate ganache and serve, or, you can refrigerate or freeze for a day or two until ready to enjoy.