Cook pasta according to package directions to al dente stage. Drain and set aside.
In a large pan, melt the butter on medium heat. Once melted, add onions and cook until translucent 3 or 4 minutes. Add the flour into the butter and whisk until combine. Cook 2 minutes on medium until lightly golden. Slowly whisk in milk until no lumps remain. reduce heat to low and season with salt, pepper and nutmeg. Simmer 2 minutes, whisking until the sauce starts to thicken. Remove from heat and add Monterrey jack cheese. Stir until cheese melts. Add pasta and stir until combined. Add butternut squash and stir until well coated being careful not to break up the squash.
Spoon mixture into an oven safe dish.
Combine melted butter and bread crumbs.
Top pasta with parmesan cheese and bread crumb mixture.
Bake at 375 degrees F for 20 to 25 minutes or until hot, bubbly and golden brown.