Preheat the oven to 350 degrees F and line a muffin tray with 12 paper liners, set aside.
Beat together all ingredients for the cream cheese batter in a medium bowl. Set aside.
In a separate medium bowl, beat together the pumpkin puree, eggs, oil, milk, and vanilla. Set aside.
In a large bowl, whisk together the flour, brown sugar, cinnamon, baking powder, nutmeg, baking soda, kosher salt, ground ginger, and allspice.
Add the pumpkin mixture to the flour mixture and stir to combine, being careful not to over-mix.
Fill each muffin well about 2/3 full with pumpkin batter, reserving about 6 tablespoons of pumpkin batter for the top.
Divide the cream cheese batter on top of the muffins, and then add about 1/2 tablespoon of pumpkin batter on top of each. Sprinkle on the sunflower seeds.
Bake until a toothpick inserted inside comes out clean or with just a couple of crumbs, about 20 to 25 minutes.
Cool completely. Store leftovers covered at room temperature for up to 3 days.