Place a pizza stone on the middle oven rack and preheat to 500 degrees F. Line a baking sheet with parchment paper and place it on top of the pizza stone.
Warm the olive oil in a small skillet or saucepan over medium heat. Add the rosemary, thyme, red pepper flakes and garlic. Remove from the heat and let cool slightly. Stir in the parsley and season with salt. Set aside.
Cook the bacon in a medium skillet over medium-low heat, turning occasionally, until crisp, about 10 minutes. Drain on a paper towel¿lined plate, then crumble.
Lightly dust a work surface with flour. Flatten each piece of dough and shape into a 3 1/2-inch round. Spread 1/4 teaspoon tomato paste in the center of each round, leaving a small border around the edge. Tear the basil into pieces; add to the center of each round, along with about 1 teaspoon crumbled bacon each. Top each with a few cubes of mozzarella. Season with salt and red pepper flakes. Very lightly brush the edge of the dough with water. Bring the edge of the dough toward the center, lightly pleating to form a tight enclosure; pinch to seal. Place seam-side down on a sheet of parchment paper. Using a metal skewer dipped in flour, make a hole in the center of each dough ball to create a steam vent.
Remove the hot baking sheet from the oven, then carefully place all the dough balls on it, spacing them 2 inches apart. Brush them liberally with the herb oil. Transfer the baking sheet to the pizza stone and bake 5 minutes. Rotate the pan and bake until the dough is golden brown, about 10 more minutes. Remove from the oven and brush with more herb oil. Serve immediately with marinara sauce and the remaining herb oil for dipping.