Turn the oven on to broil. Place the poblano pepper on a baking pan and broil until blackened, turning to broil all sides. Remove from the heat and place in a paper bag to steam. Once cooled, scrape off the blackened skin, remove seeds and dice the flesh. Set aside.
Heat the oven to 425° F. Toss the butternut squash with olive oil, salt, pepper, oregano, cayenne, cumin and rosemary. Spread out on a baking pan either sprayed with cooking spray or covered with parchment. Bake for 20 minutes, stirring once, or until browned and tender. Set aside.
Begin heating a large pot of water with 2 to 3 quarts of generously salted water. Slice the bacon in ½ inch strips and sauté in a medium skillet until browned and crisp. Remove to a paper towel to drain. Pour off the bacon fat, leaving one tablespoon in the skillet. When ready to make the sauce, heat the bacon fat over medium high heat until sizzling, then stir in the flour until smooth. Gradually add the milk, stirring constantly until it comes to a boil. Turn heat down and simmer sauce for 1 minute. Add the grated cheese and season to taste. Stir in the diced poblano.
When the water is boiling, cook the pasta according to the recipe or package directions. When al dente drain the pasta, reserving ½ cup starchy cooking water. Toss pasta with the sauce, butternut squash and bacon slices, adding starchy cooking water as needed to thin the sauce.