In a bowl, combine pumpkin puree, sugars, eggs, vanilla, and butter.
Add in the dry ingredients: flour, baking soda, baking powder, salt, cinnamon, pumpkin pie spice, nutmeg, and ginger. Fold together, but do not overmix.
For the cream cheese mixture, add room temperature cream cheese, sugar, vanilla, and salt in a bowl and mix until smooth.
Space out the muffins in the prepared muffin pan and fill the liners all the way to the top.
Pipe the cream cheese mixture into the center of each muffin, bringing it up to the top and leaving a dollop on top.
Add chopped pumpkin seeds to the perimeter of the muffins.
Bake at 350°F for 25 minutes.
