Fill a large pot with lightly salted water and bring to a rolling boil over high heat. Once the water is boiling, stir in the penne, and return to a boil. Cook the pasta uncovered, stirring occasionally, until the pasta has cooked through, but is still firm to the bite, about 11 minutes. Drain well in a colander set in the sink.
Place the bacon in a large, deep skillet, and cook over medium-high heat, turning occasionally, until evenly browned, about 10 minutes. Drain the bacon slices on a paper towel-lined plate, and reserve the remaining bacon drippings in a small bowl. Crumble the bacon into a bowl, then mix in the panko bread crumbs, butter, and chopped parsley. Set aside.
Heat the olive oil in a skillet over medium heat. Stir in the garlic and shallots; cook and stir until the shallots have softened and turned translucent, about 5 minutes. Stir in the bacon drippings and flour. Cook and stir for 1 minute, then whisk in the heavy cream and thyme. Continue to cook and stir until reduced by 1/3. Add Monterey Jack cheese and Cheddar cheese, stirring until cheeses have melted. Season with salt and pepper. Stir in the penne pasta. Transfer the pasta mixture to a 9x13-inch baking dish. Sprinkle with the bread crumb mixture.
Bake in the preheated oven until bread crumbs have browned and the sauce is bubbly, about 25 minutes.
