Preheat oven to 180 C / Gas 4. Grease a 23x33cm or similar sized baking dish and sprinkle 1 tablespoon Parmesan cheese around the inside of the dish.
Fill a large pot with lightly salted water and bring to a rolling boil. Once the water is boiling, stir in the penne and return to the boil. Cook the penne 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 pieces into a large, deep frying pan and cook over medium-high heat, stirring occasionally, until evenly browned, about 10 minutes. Drain the bacon on a kitchen towel-lined plate. Retain 4 tablespoons of bacon drippings. Set the bacon pieces aside.
Melt butter and bacon drippings together in a large saucepan over medium heat and cook and stir the onion until translucent, about 5 minutes. Whisk in the flour, stirring frequently until the mixture forms a smooth paste. Whisk in the milk, a little at a time and bring the mixture to a simmer, whisking constantly until thickened. Stir in the thyme, salt and pepper, then whisk in 4 tablespoons Parmesan and 350g Cheddar cheese, stirring constantly until the Cheddar cheese has melted and the sauce is smooth and thick.
Stir the cooked penne pasta into the cheese sauce, then lightly mix in the cooked bacon. Spread the mixture into the prepared baking dish and sprinkle remaining Cheddar cheese over the top. Cover the dish with foil.
Bake in the preheated oven until the pasta is hot and bubbling, about 25 minutes. Remove the dish from the oven and turn on the grill. Remove the foil and grill the dish until the cheese topping is browned and crisp, about 5 minutes.