Preheat a pizza stone in a 500 degree F oven. Dust the top of a pizza peel with semolina flour, and lay the pizza dough on top.
For the sauce: Heat the oil in a medium saucepan over high heat. Cook the onions until soft, about 4 minutes. Stir in the garlic, serrano and red pepper flakes, 30 seconds. Add the tomatoes and bring to a boil, and then reduce to a simmer and cook until thickened, 20 to 30 minutes. Mash the tomatoes, using a masher. Season with salt, black pepper and honey, if using. Stir in the chopped parsley and remove from the heat.
For assembling: Ladle a thin layer of sauce onto the pizza dough, and sprinkle the sliced and grated mozzarella on top. Arrange some of the broccoli rabe over the cheese. Season with salt and black pepper and bake until the crust is golden brown and the cheese is completely melted, about 8 minutes. Arrange the anchovies on the pizza, top with the egg and grated Parmigiano-Reggiano, and garnish with chopped parsley and thyme.
Pour the warm water into a small bowl (if the water is too hot the yeast will die and if the water is too cold the yeast will not activate). Stir in the sugar and dry yeast to combine and let sit 15 minutes. The top of the water will bubble and smell very yeasty, this is what you want.
Combine the flour and salt in a large mixing bowl. Make a well in the center and pour in the olive oil and yeast water. Gradually stir the flour into the liquid, using a fork. Once most of the flour has been incorporated, turn the dough out onto a smooth, clean work surface dusted with bench flour. Use your hands to knead the dough to a smooth consistency.
Place the dough in a lightly oiled mixing bowl. Cover with plastic wrap and set in a warm place until the dough has doubled in size, at least 1 hour 30 minutes. Portion the dough and stretch to the desired size.