Bring a large pot of lightly salted water to a boil. Add penne and cook, stirring occasionally, for 2 minutes less than directed on the package, about 9 minutes. Drain penne, reserving 1 cup pasta water, rinse, and set aside.
Preheat the oven to 375 degrees F (190 degrees C). Lightly grease a 9x13-inch casserole dish.
Melt 3 tablespoons butter in a large, shallow saute pan. Stir in flour and continue stirring until golden, about 3 minutes. Gradually whisk in milk. Add minced onion, bay leaves, and cayenne pepper. Continue cooking until bechamel sauce thickens, 10 to 15 minutes. Season with 1/4 teaspoon salt.
Place the cooked pasta into a large bowl. Add bechamel sauce and mix well. Crumble the drained tuna over the pasta. Add peas and Colby-Jack cheese; mix. Thin the mixture with 2 to 4 tablespoons of the reserved pasta water. Season with pepper and remaining salt. Transfer to the prepared casserole dish.
Melt remaining 2 tablespoons butter. Add bread cubes; mix well until bread is completely coated. Stir in Parmesan cheese. Top casserole with this bread mixture and cover tightly with aluminum foil.
Bake in the preheated oven for 30 minutes. Remove foil and continue baking until top is browned and golden, about 10 minutes more.