Add 1 stick of butter to a small saucepan set over medium heat, cooking until the butter begins to brown, about 3-4 minutes. Remove from the heat and transfer to a heatproof bowl. Stick in the freezer to chill, 10-15 minutes, but no longer.
Preheat the oven to 350°F. Line a baking sheet with parchment paper.
Sift the flours, baking soda, cinnamon, nutmeg, and salt into a mixing bowl.
In a large mixing bowl, beat together the cooled browned butter, the remaining 1 stick butter, brown sugar, and sugar until combined.
Beat in the pumpkin butter, egg, and vanilla, beating until creamy. Gradually add the flour mixture and beat until combined.
Fold in chocolate chunks, oats, and pecans.
Roll the dough into 1-tablespoon-sized balls and place 3 inches apart on the prepared baking sheet.
Transfer to the oven and bake for 8 minutes. Remove the pan from the oven and tap the baking sheet on the counter 2 times to flatten them down. Return to the oven and bake another 1-2 minutes or until the cookies are just beginning to set on the edges, but still doughy in the center.
Remove from the oven and tap the baking sheet on the counter 1-2 times to flatten them down again.
Let the cookies cool on the baking sheet. They will continue to cook slightly as they sit on the baking sheet. Eat warm (highly recommended) or let cool and store in an airtight container for up to 4 days.