(not so) Perfect Chocolate Chip Cookies

I thought these sounded perfect. I followed every step and I'm not sure if they are meant to be flat, or if they are supposed to have puffed up a bit at one point? The cookies taste good, but the chocolate chips look like they are little mountains in the pool of flattened cookie dough. Definetly not something I will make again.

Perfect Chocolate Chip Cookies (from Cook’s Illustrated May/June 2009)

1¾ cups (8¾ ounces) unbleached all-purpose flour
½ teaspoon baking soda
14 tablespoons (1¾ sticks) unsalted butter
½ cup (3½ ounces) granulated sugar
¾ cup (5¼ ounces) packed dark brown sugar
1 teaspoon table salt
2 teaspoons vanilla extract
1 large egg
1 large egg yolk
1¼ cups semisweet chocolate chips or chunks
¾ cup chopped pecans or walnuts, toasted (optional)

1. Adjust oven rack to middle position and heat oven to 375 degrees. Line 2 large baking sheets with parchment paper. Whisk flour and baking soda together in medium bowl; set aside.

2. Heat 10 tablespoons butter in 10-inch skillet over medium-high heat until melted, about 2 minutes. Continue cooking, swirling pan constantly until butter is dark golden brown and has nutty aroma, 1 to 3 minutes. Remove skillet from heat and, using heatproof spatula, transfer browned butter to large heatproof bowl. Stir remaining 4 tablespoons butter into hot butter until completely melted.

3. Add both sugars, salt and vanilla to bowl with butter and whisk until fully incorporated. Add egg and yolk and whisk until mixture is smooth with no sugar lumps remaining, about 30 seconds. Let mixture stand for 3 minutes, then whish for 30 seconds. Repeat process of resting and whisking 2 more times until mixture is thick, smooth and shiny. Using rubber spatula or wooden spoon, stir in flour mixture until just combined, about 1 minute. Stir in chocolate chips and nuts (if using), giving dough final stir to ensure no flour pockets remain.

4. Divide dough into 16 portions, each about 3 tablespoons (or use a #24 cookie scoop). Arrange 2 inches apart on prepared baking sheets, 8 dough balls per sheet.

5. Bake cookies 1 tray at a time until cookies are golden brown and still puffy, and edges have begun to set but centers are still soft, 10-14 minutes, rotating baking sheet halfway through baking. Transfer baking sheet to wire rack; cool cookies completely before serving.