Preheat oven to 350 degrees F. Line a 12-cup muffin tin with liners.
In a large bowl, toss together the flour, baking soda, baking powder, salt, pumpkin pie spice, cinnamon and coconut palm sugar. Set aside.
In a medium bowl, generously whisk together the pumpkin puree, eggs, coconut oil (melted), applesauce, vanilla extract and almond milk. Once thoroughly mixed, pour the wet ingredients into the large bowl of dry ingredients and stir well. Set aside.
In a small bowl, combine the chopped pecans, coconut oil (melted), applesauce, flour, cinnamon, coconut palm sugar and almond milk. Set aside.
Scoop the cream cheese into a mixer (or whisk by hand) and whip until it has reached a creamy-like texture. Combine the egg, vanilla extract and stevia into the mixer with the whipped cream cheese and mix well. Set aside.
Scoop 3 tablespoons of the pumpkin batter into each muffin liner and smooth out. The liners should be close to halfway filled.
Layer approximately 1 tablespoon of the cheesecake filling onto the tops of the pumpkin batter and smooth out. If there is any remaining filling- fill to even out.
Add an additional 1-2 tablespoons of the pumpkin batter to each muffin tin. Yes, you will fill the muffin liners up and over. Create a slight mound (like a muffin appears) by smoothing out the tops of each. Do not be afraid to press down slightly with the spoon to make sure that each crevice of the liner is filled. Spoon the pecan crunch mixture onto the top of each and press it down a bit if you need to in order to make sure it doesn't crumble (pun intended) and fall off the top.
Bake the muffins for approximately 23-25 minutes, checking at 20 minutes with a toothpick. The toothpick should remove clean.
Remove from the oven and allow to cool slightly so that the muffins can continue cooking on the inside and set properly.