Preheat your oven to 375 degrees Fahrenheit. Line a large baking sheet with parchment paper and set it aside to have it ready for scooping the cookie dough later.
In the bowl of a stand mixer fitted with a paddle attachment, or in a large bowl using a handheld mixer, beat the firm coconut oil, dark brown sugar, white sugar, and vanilla extract on medium speed until smooth, about 2 minutes. Add in the unsulphured molasses, unsweetened coconut milk, and pure pumpkin puree, then beat again on low speed until well combined. Turn off the mixer once everything is thoroughly mixed.
In a separate bowl, whisk together the all-purpose flour, baking soda, salt, and pumpkin pie spice until well combined. This ensures your leavening and spices are evenly distributed throughout the cookies.
With the mixer on low speed, gradually add the dry ingredients from Step 3 into the wet mixture from Step 2. Mix until a very thick batter forms and all ingredients are incorporated. Then, fold in 1 1/4 cups of the chocolate chips, reserving the remaining chocolate chips for later. I always recommend folding the chocolate chips in by hand to make sure they’re spread evenly.
Scoop three-tablespoon-sized mounds of cookie dough onto the prepared baking sheet, leaving a few inches between each one. Bake in the preheated oven for 9 to 10 minutes, or until the edges are golden and the centers look soft but set. Immediately after removing from the oven, press the remaining 1/4 cup chocolate chips on top of the warm cookies and sprinkle with flaky sea salt if you like. I think that little sprinkle of sea salt really makes the chocolate flavor pop! Allow cookies to cool on the baking sheet for 30 minutes before transferring them to a cooling rack.