Preheat oven to 350°F/175°C. Line a cookie sheet with parchment paper.
Make the flax egg and set it aside.
Place the butter in a mixing bowl. Use either a handheld or stand mixer on medium speed and beat until light and fluffy. Add the sugars and beat again until light and fluffy. Add the flax egg and vanilla and beat to combine.
In a separate bowl, combine the flours, cocoa, baking soda, baking powder, and salt. Whisk to combine. Pour the flour mixture into the butter mixture. Stir to combine.
Assess your batter. If the dough seems too crumbly, add 1 tablespoon at a time (up to 2) of plant-based milk and stir to combine. Don't add too much moisture because it can create flat cooks.
Add most of the chocolate chips and some of the candies, reserving some for after baking. (I find the candies fade in color when baking so I add them to the top of cookies after baking, pressing them into chocolate chips to help them stay put once the cookies cool).
Use a cookie scoop to drop cookie dough balls on a prepared cookie sheet, at least 1 1/2 inches apart. Bake for 8 to 9 minutes. Remove the cookies from the oven and allow them to sit on the cookie sheet for up to 5 minutes.
While the cookies are still hot, press in chocolate chips on top and use the melted chocolate to add candies and sprinkles to the top of each cookie. Then transfer them to a wire rack to cool completely. You can also use the melted chocolate to add googly eyes to each cookie.