Preheat oven to 375F. Coat 6-cup baking dish with cooking spray.
In large non-stick skillet melt butter over medium-high heat. Cook butternut squash, onion, marjoram, kosher salt and pepper until mixture is just tender, 12-15 minutes, stirring occasionally.
Meanwhile, cook pasta to al dente according to package directions; drain.
Combine vegetable mixture and pasta in prepared baking dish.
Reserve 1 cup Fontina cheese.
In same large non-stick skillet heat evaporated milk until hot. Stir in mozzarella and remaining Fontina cheese. Reduce heat to medium; stir constantly until cheeses are melted and mixture is smooth, about 3 minutes.
Pour cheese sauce over pasta mixture in baking dish and toss until evenly coated.
Bake, covered, 30 minutes.
Uncover. Combine Panko and reserved 1 cup Fontina cheese. Sprinkle over pasta.
Bake, uncovered, until cheese is melted, breadcrumbs are golden and mixture is hot and bubbly, about 15 minutes.