Cook pasta in boiling water for 5 minutes. Drain and set aside.
In heavy sauce pan, melt butter. Stir in flour with a whisk and cook for 1 minute.
Stir in milk and bring to simmer. Whisk for 1-2 minutes at a simmer until thickened.
Add salt, pepper, mustard, sage and pumpkin puree. Stir well until combined.
Remove from heat and add 1 1/2 cups shredded cheese. Stir until cheese is melted.
Stir pasta in pumpkin sauce. Pour into baking dish and top with remaining cheese and flatbread crumbs.
Bake at 350 degrees for 20 minutes.