Melt the butter in a large, deep skillet set over medium-high heat. Add the shallots, leeks, garlic, 1 teaspoon salt, 1/2 teaspoon pepper, and crushed pepper flakes. Cook, stirring, until the leeks are tender, about 6 minutes.
Pour in the white wine and cook until reduced by half, 2 to 3 minutes.
Add the heavy cream, seafood stock, Dijon mustard, and lemon zest. Stir until well combined. Bring to a rapid simmer, about 2 minutes. Immediately reduce to a gentle simmer (about medium-low heat).
Pat dry the halibut filets and season the tops with the remaining 1/2 teaspoon salt and 1/2 teaspoon pepper. Nestle the fish fillets into the sauce and spoon some of the sauce over the tops of the fish. Cover and cook, simmering gently, until the fish has just cooked through and flakes easily with a fork, about 10 minutes.
Garnish with fresh dill, parsley, and a sprinkle of flaky salt. Serve alone or over rice with lemon wedges for squeezing.