Using a fork, poke a few holes in skin of squash. Place the entire squash in the microwave and cook on high power for 5 minutes. Remove squash using a towel or oven mitts and allow to cool for a few minutes. Place squash on cutting board and hold warm squash with an oven mitt (or latex dishwashing glove) and slice squash in half; scoop out seeds.
Place one squash half face down on a microwave-safe plate and microwave on high-power, 3 to 5 minutes. Reserve second squash half for another use.
Scoop cooked squash flesh out of shell and place in a blender or food processor and blend with about 3 tablespoons water until smooth; set aside. Makes about 11/2 cups puree.
In a large pot, cook penne according to directions on the regular pasta box (as it takes a little longer to cook than whole grain pasta). Drain pasta, reserving about 1/2 cup pasta water.
In the same large pot, cook the bacon over medium-high heat until browned. Remove bacon to a paper towel-lined plate, reserving bacon fat (about 1 tablespoon) in the pot.
Over medium heat, whisk the flour into the bacon fat. Slowly whisk in the warm milk and cook, stirring, until the mixture begins to bubble. Continue to cook, stirring constantly, until mixture is thick, about 2 minutes. Reduce heat to low and stir in reserved squash puree; cook until warm, about 2 minutes. Stir in cheese, thyme, salt, pepper and 1 to 2 tablespoons pasta water if sauce seems too thick. Add pasta and reserved bacon and toss gently. Serve with additional shredded cheese if desired.
For good flavor and good nutrition, use half whole grain and half regular white pasta.