Cook the fennel seeds in a small dry skillet over medium heat, stirring, until toasted, about 3 minutes. Combine the flour, water, 3 tablespoons olive oil, the yeast, sugar, kosher salt and the toasted fennel seeds in a large bowl. Mix with a wooden spoon until the dough comes together.
Turn out the dough onto a lightly floured surface, dust with more flour and knead, stretching the dough and folding it over itself, until smooth and elastic, 5 to 10 minutes (dust with more flour as needed). Transfer the dough to a lightly oiled bowl, cover loosely with plastic wrap and let rise in a warm place until doubled in size, 1 to 1 1/2 hours.
Brush the bottom and sides of a 9-by-13-inch nonstick baking dish with 3 tablespoons olive oil, letting the excess oil pool on the bottom. Transfer the dough to the prepared pan and push it to the edges with your fingers (it should almost fill the pan). Cover and let rise again until the dough is puffed and the pan is full, about 1 hour.
Uncover the dough and press deep dimples all around with your fingers. Scatter the fennel over the dough and drizzle with the remaining 3 tablespoons oil, letting some oil pool in the dimples. Sprinkle generously with flaky salt. Cover and let rise again until small bubbles appear in the dough, about 30 minutes. Meanwhile, preheat the oven to 450˚.
Uncover the dough and bake until puffed and golden brown, about 35 minutes. Let cool 5 minutes in the pan, then remove to a rack to cool completely.