Preheat oven to 425°F. Place butternut squash cubes, halved brussels sprouts, diced shallots, and chopped bacon on a rimmed baking sheet. Drizzle with 1 tablespoon olive oil and season with 1 teaspoon kosher salt and freshly ground black pepper. Toss until evenly coated and spread into a single layer without crowding.

Roast vegetables for 10 minutes, then remove from oven and toss with a spatula. Return to oven for another 10 to 15 minutes until vegetables are fork-tender with golden caramelized edges, brussels sprouts have crispy browned outer leaves, and bacon is completely crisp.

While vegetables roast, bring a large pot of water to boil and add about 1 tablespoon kosher salt. Cook pasta according to package directions until al dente (usually 10 to 12 minutes). Before draining, scoop out 1 cup of pasta water into a measuring cup and set aside.

Heat a large skillet over medium heat with remaining 1 tablespoon olive oil. Add minced garlic and red pepper flakes, cooking for 30 seconds until fragrant but not browned. Stir constantly to prevent burning.

Add drained pasta to skillet along with about two-thirds of the roasted vegetables and bacon (reserve rest for topping), shredded parmesan cheese, and fresh thyme leaves. Squeeze in lemon juice and toss everything together with tongs.

Pour in about 1/2 cup of reserved pasta water and stir continuously with tongs or wooden spoon for 1 to 2 minutes until mixture transforms into a glossy, silky sauce. Add more pasta water a splash at a time if needed to reach desired consistency. Sauce should coat pasta nicely without being watery. Taste and adjust seasoning. Top with reserved crispy vegetables and bacon, plus extra parmesan cheese.