Heat pumpkin puree in a saucepan over low heat, stirring occasionally, until condensed to about 1/2 cup, about 20 minutes. Let cool, at least 10 minutes.
Beat brown sugar, shortening, and white sugar together until smooth and creamy. Add the cooled pumpkin and vanilla extract; blend well. Sprinkle in oat flour, tapioca flour, brown rice flour, guar gum, cinnamon, and salt. Add cranberries and pumpkin seeds. Mix until dough is very stiff and dry; it should not stick to your hands. Add more flour, 2 tablespoons at a time, if needed.
Preheat oven to 350 degrees F (175 degrees C). Line a baking sheet with parchment paper.
Place golf-ball size balls of dough on the prepared baking sheet. Press tops down slightly.
Bake in the preheated oven until edges just begin to turn golden, about 12 minutes. Let cool, at least 30 minutes.
Mix confectioners' sugar and melted margarine together in a bowl. Add enough milk so that icing is spreadable but not runny. Dollop icing on top of the cookies.