Preheat your oven to 325°F. Grease or line a standard 12-cup or 24-cup mini muffin tin and set it aside.
In a large bowl, place the flour, xanthan gum, baking powder, baking soda, salt, pumpkin pie spice and granulated sugar, and whisk to combine well.
Add the brown sugar and whisk to combine, working out any lumps in the brown sugar. Add the butter, pumpkin butter, vanilla and eggs, and beat until well-combined and smooth. The batter will be light, but scoop-able.
Fill the prepared muffin cups about 2/3 of the way full, and place in the center of the preheated oven.
Bake until golden and the top springs back when pressed gently with your fingertip (about 10 minutes for miniatures, 18 minutes for standard size). Remove the cupcakes from the oven and allow to cool in the pan for 5 minutes. Transfer to a wire rack to cool completely.
For the frosting.
Place the cream cheese and butter in the bowl of a stand mixer fitted with the paddle attachment. Beat on high speed until the mixture is light and fluffy (1-2 minutes).
Add the molasses, pumpkin pie spice and salt, and mix again on high until well-combined. Add the confectioner’s sugar, and mix on low speed to combine. Once the sugar has been absorbed by the butter and cream cheese mixture, add 1 tablespoon of milk and turn the mixer up to high speed and mix for about 3 minutes, or until the frosting is fluffy and thickened.
If necessary, add the remaining tablespoon of milk and continue to beat until the frosting is fluffy. Transfer frosting to a pastry bag fitted with a small tip, and pipe a generous amount of frosting on top of each cooled cupcake.
For the icing/glaze
For the pumpkin glaze, place the confectioners’ sugar in a small bowl, and add about 1 tablespoon of the pumpkin butter. Mix until it resembles a very thick paste.
Add more pumpkin butter by the half teaspoon as necessary to create that thick paste. It should be difficult to stir. Add water by the literal drop, and mix completely, until the glaze is thickly pourable.
Spoon the thick glaze on top of each cooled cupcake, and spread with a moistened offset spatula. Allow to set at room temperature before serving.