In a small bowl, stir together the flax meal and water and then set it aside to gel for 5 minutes. Meanwhile, use a handheld mixer or a stand alone mixer using a paddle attachment to beat together the vegan butter, brown sugar and cane sugar until light and fluffy, about 1-2 minutes.
Add in the flax mixture and vanilla and beat until well combined. Finally add in the pumpkin puree and mix just until combined.
In another bowl, stir together the gluten free all purpose flour, baking powder, baking soda, spices and salt. Slowly add the dry ingredients to the wet ingredients and mix until combined and a dough forms. Fold in the chocolate chips.
Use a 1 1/2 inch cookie scooper to make 14 evenly sized cookie dough balls. Place the balls on a baking sheet lined with parchment paper. Cover and freeze for at least 2 hours.
Preheat the oven to 350 F and prepare a new baking sheet with parchment paper. Place the cookie dough balls on the baking sheet about 2 inches apart. Bake the cookies for 11 minutes and the edges are golden brown. Right when you remove them from the oven, lift the pan about 5 inches from your countertop and drop the pan so the cookies spread. Repeat this 2-3 times. Return to the oven and continue baking for an additional 2-3 minutes and the edges are golden brown. Let the cookies cool on the baking sheet for 10 minutes before transferring them to a cooling rack to continue cooling. Sprinkle with flaky sea salt and enjoy!