In a medium bowl, combine the room temperature cream cheese and powdered sugar with an electric beater, until smooth. Transfer the soft mixture to a piece of parchment paper and form it into a log, even thickness (about 1 1/2 inches in diameter) and about 16 inches long. Wrap up the log and freeze for 1-2 hours.
Preheat oven to 350°F/175°C. Prepare two standard muffin pans, either nonstick spray or paper liners.
MUFFINS:
In a medium bowl, whisk together the 3 cups flour, cinnamon, nutmeg, cloves, pumpkin pie spice, salt, and baking soda.
In a large bowl, whisk together the eggs, oil, applesauce, sugar, and pumpkin puree, until well combined. Add the dry ingredients and whisk until just combined. Don't over mix - some lumps are ok.
TOPPING:
In a small bowl, add the sugar, flour, cold butter, and cinnamon. Use a pastry blender, two forks, or electric mixer to combine until crumbly.
Spoon a small amount of batter into each muffin cup, just enough to cover the bottom of the cup.
Remove the cream cheese log from the freezer and slice it into 24 equal sections. Place one section/slice in each muffin cup, on top of the bottom layer of batter. Then spoon additional batter to fill the remainder of the muffin cup about 3/4 full. Sprinkle the streusel topping over the top of each muffin.
Bake for 18-20 minutes. Let cool on a wire rack before serving.