Prep your oven and pans. Position a rack in the center of the oven and preheat the oven to 350°F. Line 3 half sheet pans with parchment paper.
Mix the dry ingredients. In a medium bowl, whisk together the flour, baking soda, and salt.
Cream the butter and sugar, then mix in the pumpkin, egg yolk, vanilla, and dry ingredients. In the bowl of a stand mixer fitted with the paddle attachment, combine the butter and sugar. Beat on medium-high until light, fluffy, and doubled in volume, 2 to 3 minutes, using a rubber spatula to scrape down the bottom and sides of the bowl as necessary. Reduce the mixer to low and add the pumpkin, scraping down the bottom and sides of the bowl after combined. Add the egg yolk and vanilla and beat until just combined. Scrape down the bottom and sides of the bowl.With the mixer on low, gradually add the dry ingredients and beat until just combined. Scrape down the bottom and sides of the bowl once more, and beat on low for an additional 30 seconds. Divide the dough. Use the rubber spatula to scrape the dough out onto a work surface and shape it into a rough ball. Use a bench scraper to divide it into three equal portions weighing roughly 12 ounces (340 grams) each. Make the pumpkin dough. Place one third of the dough back into the mixer and add the orange food coloring. Beat on low speed until just combined. Remove the dough and wipe down the inside of the bowl with a paper towel.
Make the pumpkin spice dough. Place another third of the dough back into the mixer and add the pumpkin pie spice and cinnamon. Beat on low speed until just combined. Remove the dough and wipe down the inside of the bowl with a paper towel.
Make the chocolate dough. Place the final third of the dough back into the mixer and add the cocoa powder. Beat on low speed until just combined.
Prep the cookies for shaping. Use a 1-Tablespoon cookie dough scoop to portion the pumpkin (orange) cookie dough into 18 balls. Wipe down the inside of the cookie dough scoop with a paper towel, then use the scoop to portion the pumpkin spice (light brown) cookie dough into 18 balls. Wipe down the inside of the cookie dough scoop once more, then use the scoop to portion the chocolate (dark brown) cookie dough into 18 balls. Shape the cookies. Take a pumpkin (orange) cookie dough ball, a pumpkin spice (light brown) cookie dough ball) and chocolate (dark brown) cookie dough ball and press them gently together. Roll between your palms (like you would a ball of Play-Doh) for a few seconds to combine the dough. Toss the resulting cookie dough ball in a shallow bowl filled with the remaining 3 Tablespoons of granulated sugar, covering it completely. Repeat with the remaining cookie dough balls.
Bake the cookies. Place the coated cookies at least 3 inches apart on the prepared sheet pans. Gently pat each cookie with your palm to flatten slightly.Bake one pan at a time for 10 minutes, or until the edges have set but the centers are still gooey. The cookies will look puffed when you pull them out of the oven, but will fall and crack into the perfect cookies as they cool. Cool the cookies on the pan on a wire rack for 20 minutes or until the edges and bottoms of the cookies have set and feel firm to the touch. Repeat with the remaining cookie dough. Serve and store. Serve warm, or at room temperature. The cookies can be stored in an airtight container or a zip-top bag at room temperature for up to 2 days.