Heat the olive oil in a large, deep saucepan set over medium heat until the oil shimmers. Add the leeks, season with the salt and pepper, and cook, stirring occasionally, until the edges are beginning to brown, 5 to 7 minutes; be careful not to allow them to burn.
Reduce the heat to low, cover and cook, stirring occasionally, until leeks are completely softened and somewhat translucent, 28 to 30 minutes. Uncover and reduce the heat to the lowest setting on your stove. Add the garlic. Cook, stirring frequently, until any liquid released by the leeks while cooking has been almost fully absorbed, another 2 to 3 minutes. Transfer to a container and set aside.
Preheat oven to 475 degrees
Divide the pizza dough into 2 even pieces. Stretch each piece of dough in a circular motion, then lay them both out on a flat surface and flatten out using a rolling pin. If you have a pizza peel, sprinkle some flour on it and place the stretched out dough on the peel.
Once your 2 pizza doughs are flat and ready to be heated, use a spoon to spread about ¼ cup of leek confit all around the dough leaving a little bit for the crust.
Top each pizza with half of the shredded cheese, fresh mozzarella and season with salt, pepper and red pepper flakes. Transfer the pizzas into the oven and bake for 12-13 minutes until the crust is perfect.
Remove pizza from the oven. Adjust seasoning as needed, add arugula, squeeze lemon juice on top and serve.