Heat olive oil in a large skillet or paella pan over high heat. Cook and stir onion, tomato, salt, and smoked paprika into the hot oil until softened, about 3 minutes. Add romano beans, butter beans, and rice; cook and stir until rice is coated with oil, 2 to 3 minutes.
Place shrimp, mussels, and clams over the top of the rice mixture. Pour in white wine and seafood stock; sprinkle in saffron threads and rosemary. Bring mixture to a simmer. Turn shellfish and continue to cook until clams and mussels have opened, and shrimp are pink and cooked through, about 5 minutes. Remove clams, mussels, and shrimp and set aside.
Stir peas into the paella; simmer, uncovered, until rice is tender and has absorbed the liquid, 20 to 25 minutes. Stir in squid, and return clams, mussels, and shrimp to the pan. Cook until squid is opaque and cooked through, 2 to 3 more minutes. Serve with lemon wedges and chopped parsley.