Preheat oven to 375°F. Line baking sheets with parchment paper.
In a large bowl, whisk together rolled oats, flour, cinnamon, baking powder, baking soda, salt, and nutmeg. Set aside.
In a stand mixer with paddle attachment (or large bowl with hand mixer), beat butter and brown sugar on medium until smooth and creamy, about 2 to 3 minutes.
Add eggs one at a time, beating well after each addition. Mix in vanilla and molasses until fully combined.
With mixer on low, gradually add the dry ingredients until just incorporated; don't overmix.
Stir in chocolate chips, pecans, and coconut by hand (or on very low speed) until evenly distributed.
Using a 2-tablespoon scoop, drop dough onto prepared sheets, spacing cookies 2 to 3 inches apart.
Bake 9 to 11 minutes, until edges are set and lightly golden but centers still look soft. (They will firm up as they cool.)
Sprinkle the warm cookies with flaky sea salt. Let them rest on the baking sheet for 2 to 3 minutes before transferring to a wire rack to cool completely.