Heat a drizzle of olive oil in a large pot over medium heat. Add onions, fennel, and a big pinch of Kosher salt and cook, stirring occasionally, for 10 minutes, until translucent (lower the heat and add a splash of water if browning too quickly).
Add garlic and cook, stirring often, for 30 seconds. Then add red pepper flakes and saffron (and 1 tablespoon tomato paste if not making your own stock) and cook, stirring often, for another 30 seconds.
Add white wine and cook, scraping any brown spots from the bottom of the pot, until reduced by half.
Add stock, crushed tomatoes, bay leaf, thyme, and 1 teaspoon Kosher salt and bring to a boil. Cook for 30 minutes, until slightly thickened, skimming any fat from the top. Taste and season with Kosher salt and freshly ground black pepper (the broth needs to be seasoned before the fish is added).
Add clams and cook until most of the clams have opened, 2 minutes. Add the sea bass, lobster, shrimp, and bay scallops and cook until tender, 2-3 minutes.
Remove from heat. Taste and season again with Kosher salt and freshy ground black pepper, if needed.
Serve immediately, sprinkled with dill.