To heat the flour, place it in a microwave safe bowl and microwave in 30 second increments, stirring after each, until an instant read thermometer stuck into a few different spots of the flour reaches 180 degrees F. Let cool.
Preheat the oven to 375 degrees F. Line two baking sheets with parchment paper and set aside.
In a medium bowl, whisk together 3 cups of the flour, salt, baking powder and baking soda.
In the bowl of a stand mixer fitted with the paddle attachment, cream together the butter, cream cheese and granulated sugar until fluffy, 3 to 4 minutes. Add the applesauce and mix until combined. Mix in the vanilla and almond extracts. Add the dry ingredients and mix until combined. Divide the dough among 3 bowls and add food coloring, keeping the colors separate. Wearing disposable gloves, knead in the color by hand, or stir it in with a spatula, until homogenous. If you don't have gloves, you can use a zip-top plastic bag.
You can play with and bake the dough now (dust with a little more flour if it gets sticky) or you can put it in an airtight container and refrigerate for an hour or overnight to play with and bake later.
Roll each batch of dough into a log about 2 1/2 feet long and 1 inch wide. Line up the three logs of dough and cut each into 6 equal portions. Twist one portion of each of the colored doughs together and roll into a ball to create the desired tie-dye pattern. Roll in sanding sugar, place on the prepared baking sheet and gently press down using your hand. Repeat with the remaining dough, placing the finished cookies an inch apart. Bake until very lightly browned on the bottom but still gooey on the inside, about 10 to 12 minutes. Let cool slightly and enjoy!