Put clams in a 5- to 6-quart pan and add 1 cup wine. Cover and bring to a boil over high heat; reduce heat and simmer until clams have opened, 8 to 10 minutes. Remove from heat. Using tongs, lift clams out; extract meat and put in a small bowl. Reserve some of the shells for garnish if desired. Slowly pour clam juice into another small bowl, leaving grit behind; rinse pan.
Combine red pepper, onion, and butter in pan; stir often over high heat until vegetables are limp, 5 to 8 minutes. Add mustard seeds, lemon peel, and thyme.
Pour remaining 1 cup wine and juice from clams into a 2-quart glass measure; add enough broth to make 8 cups total. Pour into pan.
Bring mixture to a boil over high heat. Add penne, reduce heat, and simmer, stirring occasionally, until pasta is tender to bite, about 10 minutes. Mix in clams, remove from heat, and let stand, uncovered, 5 to 8 minutes.
Ladle pasta and liquid into wide soup bowls; add a few clam shells to garnish if desired. Sprinkle with parmesan to taste, then top with parsley.