Stir the ground flaxseed meal and water together in a small bowl. Leave the mixture undisturbed for 10–15 minutes, allowing it to thicken into a gel-like flax egg.
While the flax mixture rests, preheat the oven to 350°F (175°C). Cover a large baking sheet with parchment paper.
Place the almond butter or cashew butter, blotted pumpkin purée, coconut sugar or maple sugar, and vanilla extract in a large mixing bowl. Stir until the ingredients are thoroughly incorporated.
Add the thickened flax egg to the pumpkin mixture. Continue stirring until the wet mixture appears smooth and evenly blended.
In a separate bowl, whisk together the almond flour, baking soda, sea salt, cinnamon, and pumpkin pie spice.
Gradually add the dry ingredients to the wet mixture, stirring until a thick, cohesive cookie dough forms.
Fold most of the dairy-free chocolate chips or chopped dark chocolate into the dough, reserving a small portion for decorating the tops. Mix gently by hand to minimize breakage.
Using a medium cookie scoop or approximately 1 1/2 tablespoons of dough per cookie, arrange the portions on the prepared baking sheet. Leave about 2 inches of space between each mound.
Because the dough will spread very little during baking, press each portion into a disc measuring approximately 1/2 to 3/4 inch thick. Press several reserved chocolate chips into the surface of each cookie.
Bake for 10–12 minutes, or until the cookies are just set. For softer, fudgier centers, remove them while they still appear slightly underbaked. Depending on the size of the baking sheet, the dough may require two batches.
Leave the cookies on the baking sheet for 5–7 minutes so they can firm up without crumbling. Carefully transfer them to a wire rack and allow them to finish cooling.