I'm not sure if it's either too thick, not baked alone long enough, or a reactuon to adding a hand made sauce....
Well, first things first... as I mentioned in my comment, tapioca flour gets gummy when heated. That's expected. In Brazil we do have something called just tapioca, and otherwise known as tapioca crepe that's made with hydrated tapioca flour spread on a pan and heated until all it sticks together and forms a "crepe" of sorts Picture here, so you can see the gummy inside
One more thing about expectations: your recipe is for a crispy crust, it will not get to the same texture as "regular" pizza crust (elastic and fluffy).
A few ways for you to lessen the gummy texture
- Add a leavening agent like baking powder or baking soda. This will aerate the mixture and prevent the tapioca flour from gelatinizing;
- Flip the dough and add the toppings on the side that was in contact with the pan. You know how the cake usually crusts on the bottom and the sides? That will protect your dough from moisture a little bit more.