Cut the butternut squash into a 1/4-1/2-inch dice. (Cut it on the smaller side if you want the squash to completely mash into the sauce or on the larger side if you still want pieces of squash in the finished dish.)
Heat a large pot or Dutch oven over medium heat. Add the oil and butter. Once the butter is melted, add the squash, garlic, and thyme/sage. Sprinkle with 1 teaspoon of salt. Cook, stirring frequently, until the garlic is lightly toasted, about 2 minutes.
Add the pasta, milk, and water/broth to the pot. Stir to combine. Bring the pot up to a simmer then cover and cook, stirring every few minutes, until the pasta is al dente, 10 to 12 minutes (depending on the shape of the pasta).
Once the pasta is cooked, stir in the yogurt/cream cheese, cheese, and remaining 1/2 teaspoon of salt. Taste and add more salt and pepper as needed.
The mac and cheese is best served right away. It will get thicker as it sits, so stir in a splash more milk if you need to loosen up the sauce again.