Combine almond flour, coconut flour, arrowroot flour, 1 teaspoon salt, baking soda, and xanthan gum in a medium bowl. Whisk until thoroughly combined.

Cream butter in a large bowl using an electric mixer. Add sweetener and molasses; continue to beat until thoroughly mixed and much of the sweetener has dissolved. Add vanilla extract and egg, mixing until just incorporated; the mixture will not be totally smooth.

Add 1/2 the flour mixture to the bowl with the butter mixture; mix on low until just incorporated. Mix in remaining flour mixture. Fold in chocolate chips and pecans. Cover the bowl and refrigerate for 1 hour.

Preheat the oven to 350 degrees F (175 degrees C). Line a baking sheet with parchment paper or a silicone baking mat.

Divide cookie dough into 12 portions, form into rounds, and flatten to 2 1/2 inches in diameter; cookies will spread slightly during baking. Place cookies on the prepared baking sheet.

Bake in the preheated oven for 6 minutes. Sprinkle cookies with sea salt and flip tray around in the oven. Continue baking until just set and still soft to the touch, another 6 to 7 minutes. Allow cookies to cool completely on the baking sheet. Store in an airtight container for up to 3 days.