Prepare the springform pan for a water bath. Once the crust has cooled, wrap the springform pan with 2 layers of heavy-duty foil wrapping and folding the edges at least ¾ up the sides of the pan. For an extra barrier, if desired, place an oven bag around the foil and tie it around the foil to secure it.
Combine the softened cream cheese and sugar in the bowl of a stand mixer with a paddle attachment (or use a hand mixer) and mix on medium until smooth, about 2-3 minutes scraping the sides of the bowl occasionally.
Add the eggs one at a time, mixing well after each.
Add the eggnog, bourbon, and vanilla and mix well.
Add the flour, nutmeg and salt and mix until combined, about 10 seconds.
Pour the batter into the prepared pan over the crust. If you have too much batter or your crust wasn’t pushed up the sides far enough, only fill until the batter is at the top of the crust. Either discard the additional batter or make individual cheesecakes using paper cups in a muffin tin and baking for about 25-30 minutes or until they are almost set in the middle.
Place the springform pan into a roasting pan and place in the oven. Carefully pour very hot water into the roasting pan until it comes about halfway up the sides of the springform pan being careful not to get any water between the pan and the foil.
Bake the cheesecake at 325 degrees 80 to 90 minutes. The cheesecake is done when the middle is still slightly jiggly but the edges are fully set.
Turn the oven off and slightly prop open the oven door with a wooden spoon if it won’t stay open on its own. Allow to cool in the oven for 1 hour.
Carefully remove the roasting pan from the oven and remove the cheesecake from the water. Remove the foil. Cool for another hour on a wire rack.
Place the cheesecake in the refrigerator, covering the top with foil or plastic wrap and chill at least 4 hours or overnight.