1. Preheat oven to 350°F (175°C).
2. Combine graham cracker crumbs, sugar, and nutmeg in a medium bowl.
3. Mix in melted butter until well combined.
4. Press mixture into the bottom of a 9-inch springform pan.
5. Bake crust for 8-10 minutes, then let cool slightly.
6. Reduce oven temperature to 325°F (160°C).
7. Beat cream cheese until smooth in a large mixing bowl.
8. Add sugar, flour, nutmeg, cinnamon, cloves, and salt; mix until combined.
9. Beat in eggs one at a time, mixing just until incorporated.
10. Stir in eggnog, vanilla bean paste, and dark molasses + apple juice (if using).
11. Pour cheesecake batter over the cooled crust.
12. Place springform pan in a larger roasting pan.
13. Pour hot water into the roasting pan, halfway up the sides of the springform pan.
14. Bake for 60-75 minutes until edges are set and center jiggles slightly.
15. Turn off oven, crack door open, and let cheesecake cool for 1 hour.
16. Remove from water bath and cool completely on a wire rack.
17. Refrigerate for at least 6 hours or overnight.
18. For topping, beat whipping cream, powdered sugar, and vanilla bean paste until stiff peaks form.
19. Top cheesecake with whipped cream and garnish with grated nutmeg before serving.