Place bacon in a small skillet over medium heat; cook, stirring, until golden and crisp, 6 to 8 minutes. Transfer to paper towels to drain; set aside to cool.
In the bowl of a stand mixer, dissolve yeast in 2 1/4 cups warm water (110°F.) Add flour and stir until well combined. Cover and let stand in a warm, draft-free area until bubbling and doubled in volume, about 2 hours. Add salt and bacon to dough and mix with the dough hook on low speed until loose and sticky, about 5 minutes. Increase speed to medium and mix 30 seconds. Turn dough out onto a well-floured work surface. Fold top half of dough down toward center and pat gently to deflate. Rotate 90 degrees and repeat. Continue to rotate dough, fold down, and pat to deflate until you have folded each side of dough. Repeat 5 more times. Gently transfer dough to an oiled bowl, folded-side down. Cover and let rest until doubled in volume, about 1 hour.
Preheat oven to 450°F with a pizza stone or baking sheet on the lower third rack; heat for at least 1 hour. In a small bowl, toss tomatoes with garlic, thyme, red pepper flakes, and 1 tablespoon oil. Drizzle remaining 1/3 cup oil over the surface of a 13-by-18-inch rimmed baking sheet. Turn dough out onto baking sheet and, using oiled fingertips, press dough outward to reach edges. Scatter tomatoes over dough, pressing gently to adhere. Cover and let rest until puffy, about 45 minutes (press dough toward edges if it begins to shrink back.)
Generously sprinkle dough with flaky salt. Bake, rotating pan halfway through, until puffed and golden brown on top and bottom, 25 to 35 minutes. Carefully slide bread out of pan onto a wire rack. Sprinkle with more flaky salt. Let cool slightly; serve warm or at room temperature topped with arugula.