Preheat the oven to 350°.
In a large bowl, whisk together flour, cocoa powder, baking soda, baking powder, and kosher salt. Set aside.
In a stand mixer fitted with a paddle attachment, cream coconut oil, sugars, and vanilla until fluffy, stopping once to scrape down the sides of the bowl. Add eggs and mix until well incorporated. With the mixer on low, slowly add dry ingredients and mix until well combined. Pour in chocolate chunks and mix for another 15 seconds.
Using a cookie scoop, place about 2 tablespoons of dough onto a baking sheet lined with parchment paper. The cookies will spread, so make sure to leave enough space for each cookie. Sprinkle with sea salt and dried flowers or berries, if using. Bake for 8–10 minutes until the middles are set. Cool cookies completely before transferring them to a plate. Store in an airtight container.