Preheat oven to 200°C (180ºC fan). In a large ovenproof pan or medium baking dish, combine tomatoes, shallot, garlic, and most of the olive oil. Season with salt and chilli flakes and toss to combine.
Place feta into centre of tomato mixture and drizzle top with remaining olive oil. Scatter thyme over tomatoes. Bake for 40 to 45 minutes, until tomatoes are bursting and feta is golden on top.
Meanwhile, in a large pot of salted boiling water, cook pasta according to package instructions. Reserve 120ml pasta water before draining.
To pan with tomatoes and feta, add cooked pasta, reserved pasta water, and lemon zest (if using) to pan and stir until completely combined. Garnish with basil before serving.