Preheat oven to 350 degrees. Grease a muffin tin with non-stick spray or line with cupcake liners.
Make the flax eggs: mix 2 Tbsp of flaxseed meal with 6 Tbsp of water, then let sit for 10 minutes to thicken.
In a large mixing bowl, combine the flax eggs, pumpkin puree, avocado oil, dark chocolate almond milk, maple syrup, and vanilla extract. Mix until well combined.
Add the baking soda or baking powder, oat flour, and cocoa powder to the same bowl and fold them into the wet mixture. Mix until all the chunks have been smoothed out. This will be a thicker batter. Fold in the chocolate chips.
Evenly distribute the batter between the lined cups in the prepared muffin tin. Shake the tin to even out the batter, then sprinkle extra chocolate chips on top of each muffin.
Bake for 20 minutes, then let cool for 5-10 minutes. Sprinkle with flakey sea salt.