Fill a large saucepan with lightly salted water and bring to a rolling boil over high heat. Stir in the penne then 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.
Place the bacon in a large frying pan 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 grease 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 frying pan over medium heat. Stir in the garlic and eschalots; cook and stir until the eschalots have softened and turned translucent, about 5 minutes. Stir in the bacon grease and flour. Cook and stir for 1 minute then whisk in the thickened cream and thyme. Continue to cook and stir until reduced by 1/3. Add mozzarella 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 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.