Whisk the warm water, sugar, and instant yeast together in a glass measuring cup. Proof for 2-3 minutes to ensure the yeast is active. You should start to see small bubbles on the surface of the mixture (Note 4).
Add the gluten-free flour, almond flour, baking powder, kosher salt, and tapioca powder to the bowl of a stand mixer with the paddle attachment (Note 5). Mix on low speed for 1 minute to combine.
With the mixer running on low speed, slowly pour in the yeast mixture and then the olive oil. Increase the speed to medium-high and beat for 2-3 minutes. It should resemble a cookie dough and will not be sticky and stretchy like traditional pizza crust.
Scrape the sides of the bowl using an oiled spatula and form the dough into a ball in the center of the bowl. Cover with a kitchen towel and allow it to rest and rise in a warm place for 30 minutes.
Preheat the oven to 425°F. Oil a large sheet pan with olive oil. Using oiled hands, press the dough into the pan in an even layer to all 4 corners of the pan. Let the dough rest for another 15 minutes.
Bake in the preheated oven for 10 minutes.
While it’s baking, mix together the garlic, basil, red pepper flakes, salt, and pepper.
Carefully remove the crust from the oven and sprinkle on the herb mixture. Pour the pizza sauce on top and use the back of a spoon to spread the pizza sauce, spreading the herb mixture as well. Top with the cubed mozzarella, pepperoni, and then shredded cheese.
Bake for another 15-17 minutes, until the crust is slightly browned and the cheese is melted and bubbling. Check the pizza and turn the pan as needed for even cooking. Cool slightly, slice, and serve with more fresh basil, parmesan cheese, or red pepper flakes.