In a large pot of boiling water, cook the butternut squash and matchstix carrots until tender, about 10-12 minutes. Strain and transfer them to a high-powered blender. Process until completely smooth and set aside.
In a large pot of salted boiling water, cook the pasta according to the package instructions until al dente. Drain and set aside. Return the pot to the stovetop.
Melt the butter over medium heat. Add flour and whisk continuously for 1-2 minutes to form a roux. Gradually pour in the milk, whisking constantly to prevent lumps. Stir in the shredded cheddar cheese and onion powder, whisking until the cheese is melted and the sauce is smooth.
Stir in the pureed vegetables and mix well to combine. Season with Kosher salt and freshly cracked black pepper to taste.
Toss the cooked pasta in the cheese sauce and mix until fully coated. If desired, sprinkle with toasted breadcrumbs before serving.