Roast squash with olive oil, salt, and pepper at 425°F for 20 to 25 minutes, flipping once.
Cook onion in 1 tbsp butter over medium-low heat for 20 to 25 minutes until deeply golden.
Melt remaining butter, add garlic, then clam juice and lemon juice. Bring to a simmer.
Add clams, cover, and steam 5 to 7 minutes until open. Discard any unopened. Remove meat, reserve broth.
Top flatbreads with onions, squash, clam meat, and cheese.
Bake at 425°F for 8 to 10 minutes until cheese is melted and edges are crisp.
Drizzle with reserved broth, garnish with thyme and pepper flakes, and serve with lemon wedges.