Preheat oven to 420F (215C) and line a 12-cup muffin pan with cupcake liners.
To make the filling: Microwave cream cheese in a microwave-safe bowl on low power for 30 seconds. Add the sugar and vanilla extract and whisk until smooth. Transfer to a piping bag (without a tip) and set aside.
To make the pumpkin praline topping: In a small bowl combine 1/4 tsp pumpkin pie spice and 1 Tbsp brown sugar. Set aside. Melt butter in a small skillet over medium heat. Add pumpkin seeds and cook for 2-3 minutes, then add remaining brown sugar and cook for 1-2 minutes stirring constantly until caramelized. Transfer caramelized pumpkin seeds to brown sugar mixture and stir to combine. Set aside.
In a medium bowl combine flour, salt, baking powder, baking soda, and pumpkin spice. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment combine softened butter and sugar, beat at medium speed for 1 minute. Add eggs and beat for 2 minutes at high speed. Reduce speed to low, add pumpkin puree and mix until combined.
Add the flour mixture to the bowl and beat until just combined.
Spoon the batter into the prepared muffin pan, filling the cups all the way to the top. Sprinkle with Pumpkin Praline Topping. Cut off the tip of the piping bag and press about 2-3 Tbsp of cream cheese filling into the batter (see image above).
Bake for 5 minutes at 420F (215C), then keeping the muffins in the oven, lower the oven temperature to 350F (180C) and bake for about 20 more minutes, or until the muffins are golden on top.
Transfer the pan to a cooling rack and let the muffins cool for 5-10 minutes. Remove the muffins from the pan and let cool to room temperature on the rack.