In a medium bowl, combine the flour, salt, baking soda, cinnamon and allspice.
In a large bowl, use an electric mixer to cream the butter and both sugars until light and fluffy, about 3-4 minutes. Beat in the eggs followed by the vanilla extract. On low speed, mix the dry ingredients into the wet ingredients. Fold in the oats and chocolate chunks.
Cover the bowl and chill the dough overnight in the refrigerator.
Preheat the oven to 375 degrees. Scoop the dough into balls by the scant 1/4-cup-full. Place on a sheet pan 2 inches apart, gently flattening them with your palm.
Bake the cookies for 10-12 minutes until golden brown, rotating the sheet pans halfway through baking.
Sprinkle the cookies with flaky sea salt while they are hot. Let the cookie sit on the sheet pans for 5 minutes before transferring to a wire rack to cool completely.