First, brown the butter. When making browned butter, it is best to use a stainless steel pan so that you can see the color of the butter change. Heat the butter in a large shallow frying pan over medium heat until melted. Swirl the pan around a bit every couple minutes to help it cook evenly. Over a period of several minutes, you’ll notice the foam at the top of the butter start to change from light yellow to a dark tan. Once it reaches the dark tan stage and the butter looks light brown and golden, smell it. It should smell nutty and similar to toffee. Remove from heat and set aside to cool to warm.
In a medium bowl, mix together the graham cracker crumbs, brown sugar, cinnamon, and allspice. Add the melted butter and mix with your hands to combine. Add the eggs and milk and continue mixing with your hands until a crumbly dough mixture forms.
Line the bottom of a springform pan that's 9-inches in diameter and 2.5 inches deep with parchment paper and grease the sides. Use your fingers to press the bits of dough to the bottom of the pan to form the base of the crust, then start pressing the dough up the sides to form the crust all the way to the top of the pan. Set aside.
Preheat the oven to 300 degrees Fahrenheit with a pot of water on the lowest rack of the oven. In the bowl of a stand mixer fitted with the paddle attachment, beat the cream cheese and sugar at medium low speed until smooth and fluffy, about 1 minute. Add the sour cream and beat until smooth, then add the yogurt and beat until combined. Add the eggs, one at a time, mixing well after each addition. Then add the milk, vanilla extract, cinnamon, ginger, allspice, and nutmeg and continue beating until smooth and completely combined. Set aside.
Arrange the apple slices in the pan to create a flower shape, starting around the edge of the pan and working your way inward. Don't pack them too tightly, you want the batter to be able to seep between the apple slices. Pour the batter into the pan, pouring into different areas of the pan to help it spread evenly between the apple slices.
Place the pan on a large lipped baking sheet and place it in the center rack of the oven. Bake until the edges of the cheesecake are set but the center is still slightly wobbly and the exposed portions of the apple slices are golden, about 1 hour and 30 minutes. Turn the oven off, open the oven door, and allow the cheesecake to cool to room temperature over a period of 3 hours (this helps prevent cracking on the top of the cake, read the blog post above for more cracking-prevention tips). Slice and enjoy!