Line a 9×13-inch baking pan with parchment paper, leaving an overhang on the long sides to lift the bars out later. Lightly spray the parchment and sides with nonstick spray. Preheat the oven to 325°F (163°C).

In a medium bowl, combine graham cracker crumbs, granulated sugar, brown sugar, cinnamon, nutmeg, and salt. Add the melted butter and mix until evenly moistened and the mixture resembles wet sand.

Pour the crust mixture into the prepared pan. Press firmly and evenly across the bottom using your fingers and the bottom of a measuring cup or glass. Bake for 10 minutes, then remove from the oven and let cool slightly while you prepare the filling.

In a large mixing bowl or stand mixer fitted with the paddle attachment, beat the softened cream cheese on medium speed for 2–3 minutes until very smooth and fluffy. Add the granulated sugar and brown sugar and beat for another 2–3 minutes, scraping down the sides and bottom of the bowl to eliminate lumps.

Add the eggs and egg yolk one at a time, beating on low speed just until each is incorporated. Avoid whipping in too much air and scrape the bowl as needed.

Add the eggnog, vanilla, nutmeg, cinnamon, flour, and salt. Mix on low speed until the batter is smooth and well combined. The batter will be slightly looser than traditional cheesecake due to the eggnog.

Place the 9×13-inch pan on a large rimmed baking sheet to help buffer the heat and promote even baking. For a classic water bath, set the pan inside a larger roasting pan and pour hot water around it halfway up the sides, ensuring the pan is leak-proof or well wrapped in foil.

Pour the eggnog cheesecake batter over the partially baked crust and smooth the top with a spatula. Bake at 325°F (163°C) for 35–45 minutes, until the edges are set and slightly puffed and the center still has a gentle jiggle.

Turn off the oven, crack the door slightly, and let the bars sit inside for 20–30 minutes. Remove the pan from the oven and place on a cooling rack. Cool completely to room temperature.

Once at room temperature, cover the pan and refrigerate for at least 4 hours, preferably overnight. To serve, lift the cheesecake slab out using the parchment overhang and transfer to a cutting board. Slice into bars with a sharp knife, wiping the blade between cuts. Top with whipped cream and a sprinkle of freshly grated nutmeg and crushed gingersnaps or graham crumbs if desired.