Preheat oven to 400°. In a large ovenproof skillet or medium baking dish, combine tomatoes, shallot, garlic, and all but 1 tablespoon oil. Season with salt and red pepper flakes and toss to combine.
Place feta into center of tomato mixture and drizzle with remaining 1 tablespoon oil. Scatter thyme sprigs over tomatoes. Bake for 40 to 45 minutes, until tomatoes are bursting and feta is golden on top.
Meanwhile, in a large pot of boiling salted water, cook pasta until al dente according to package directions. Reserve ½ cup pasta water before draining.
To skillet with tomatoes and feta, add cooked pasta, reserved pasta water, and lemon zest (if using) and stir until combined. Garnish with basil.
