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Preheat oven to 450 degrees. Grease a large baking sheet with olive oil.
Heat 1 tablespoon oil in a large skillet over medium-high heat. When oil shimmers, add onions and honey and cook 5 minutes, stirring occasionally until softened. Season with sea salt and pepper and continue cooking 5-10 minutes or until the onions are golden and caramelized. Remove from heat and let cool.
In medium bowl, toss together tomatoes, remaining 2 tablespoons oil, 1 tablespoon balsamic vinegar, thyme, garlic, crushed red pepper flakes and a pinch each of sea salt and pepper.
On a lightly floured surface, carefully stretch dough into a 10-12 inch circle. Transfer to prepared baking sheet. Spread the dough with crème fraîche, if using, and top evenly with onions. Add tomatoes on top.
Transfer pizza to oven and bake 10-15 minutes or until crust is golden and tomatoes are bursting. Drizzle with more balsamic vinegar and olive oil; and serve.