
Preheat the oven to 315º F. Line a muffin tin with parchment paper liners and set aside.
In a large bowl, combine flours, salt, coconut sugar, cinnamon, pumpkin pie spice, and baking soda and whisk until well combined and no lumps remain. Add in remaining muffin ingredients, except chocolate chips, and mix with a spatula until well combined.
Spoon into prepared muffin tin until almost entirely full, rounding at the top. I use a disher for this purpose. Bake at 315º F in the middle rack for 23-25 minutes, or until a toothpick inserted in the center comes out clean AND the surface of the muffin springs back when touched. Remove and let cool slightly, then transfer to a wire cooling rack to cool completely.
Meanwhile, make your cream cheese frosting. Combine all ingredients in a high-speed blender and process until very, very smooth. Chill completely.
When ready to serve, pipe frosting on muffin with a piping bag or smear on with a butter knife or offset spatula. Serve immediately.