Make the orecchiette: On a clean work surface, place the semolina and grano arso flours in a small mound, mixing to combine. Create a deep well in the center and add ⅓ cup plus 2 tablespoons lukewarm water. Using a fork and starting from the interior wall of the well, gradually incorporate the flour into the water until a thick batter-like consistency forms. Use a bowl scraper to cut and fold the remaining flour into the center until a shaggy mass forms; press to form a dough, then knead until it becomes smooth and elastic, 18-20 minutes.
Generously dust a baking sheet with semolina and set aside. Break off a piece of dough about the size of a lemon and cover the rest of the dough tightly with a sheet of plastic wrap. Roll the smaller dough piece to a long rope about ¾ inch thick; using a sharp knife, slice into disks about 1⁄16 inch thick.
One at a time, pick up a piece of dough and use the tip of your thumb to press a deep well into the center, creating a rough, half-sphere-shape that is slightly thicker at the edges. Place the finished orecchiette on the prepared baking sheet and repeat with the remaining dough pieces. Set the finished pasta aside for at least 1 hour or up to 2 days before cooking.
Set a large bowl of ice water beside the stove. Coarsely chop one of the onions. In a medium pot, combine the potatoes, celery, chopped onion, and 1 of the tomatoes and add enough water to cover by 1 inch. Season generously with kosher salt and bring to a low boil over medium-high heat. Lower the heat to maintain a simmer, and let cook for 15 minutes. Add the squid or cuttlefish and continue cooking until firm-tender, 1-2 minutes for squid or 3-4 minutes for cuttlefish. Use tongs or a slotted spoon to transfer the squid or cuttlefish to the ice water. Once cool, remove and thinly slice (discard the ice water).
Set a fine strainer over a large bowl or liquid measuring cup. Strain and reserve the broth. Discard the vegetables.
Bring a large pot of heavily salted water to a boil over high heat. Add the orecchiette and cook, stirring occasionally, until al dente, 1 ½-2 minutes (or as many as 6 minutes if completely dried). Drain the pasta and set aside while you finish the sauce.
Halve and thinly slice one of the onions. Seed and dice the remaining 6 tomatoes. In a large skillet set over medium-low heat, add 2 tablespoons olive oil. Once hot, add sliced onion and garlic, and and cook, stirring occasionally, until the onion is soft and beginning to brown, 10-12 minutes. Remove the garlic clove, add the tomatoes, and continue cooking to reduce the liquid in the tomatoes slightly, 2-3 minutes. Add the cooked orecchiette, the squid or cuttlefish, 1 cup of the reserved broth, the basil, and the red pepper flakes if using; continue cooking, stirring constantly, until the pasta is tender and the broth is slightly thickened, 2-3 minutes. Season with sea salt and freshly ground black pepper to taste, and serve immediately.