In a medium bowl, whisk together flour, ginger, cinnamon, nutmeg, pumpkin pie spice, salt, and baking soda; set aside.
In the bowl of a stand mixer, fitted with the paddle attachment (or large bowl if using a hand mixer), cream together butter and sugars on medium-high speed, about 3-4 minutes.
Add molasses and mix at medium speed until combined. Add egg and vanilla extract and mix until combined, scraping down the sides of the bowl with a spatula as necessary.
With the mixer on low, slowly add in the dry ingredients and mix until just combined, scraping down the sides of the bowl with a spatula as needed.
Use spatula to scoop dough all towards the center of the mixing bowl, then cover with plastic wrap and refrigerate for about 1 1/2 hours. Longer is ok, just make sure the plastic wrap is covering the dough so it doesn’t get hard around the edges.
Preheat oven to 350 degrees F. Line a large baking sheet with a Silpat mat or parchment paper. Place your remaining 1/3 cup of granulated sugar in a bowl good for rolling the dough balls in.
Using a medium cookie scoop or tablespoon, scoop dough and roll in your hands to make a nice ball.
Roll each ball in the bowl of sugar and place on the prepared baking sheet, 2 inches apart.**
Use a measuring spoon (teaspoon is a good size), carefully press down the center of each cookie dough ball, to make an indention (the thumbprint!), but don’t press all the way to the cookie sheet.
Bake cookies about 7-9 minutes. Cookies will still be soft, and the indented center will have puffed backup – just use your measuring spoon to press it back down while warm. Allow to cool on baking sheet for a few minutes before transferring to a cooling rack to cool completely. Make sure they are completely cooled before adding the filling.
Note: If you are making ahead and want to freeze, this is the point at which you will want to freeze the baked cookies!