Pour the rice crackers into the bowl of a food processor. Blend the crackers at 2 to 3 second intervals, until most of the crackers have broken down into crumbs or small chunks no larger than 1/4-inch wide (see photo below). I blended the crackers for about 9 seconds total. This should yield about 1/2 cup of crumbs (see note 3). If there’s 1 or 2 rice crackers that haven’t broken down properly, crush them with a kitchen mallet or eat them. Transfer the rice cracker crumbs to a bowl.
Melt the butter in a microwave or in a saucepan over the stove. Pour the melted butter over the rice cracker crumbs and use your fingers to work the butter into the crumbs. You can also use a spoon or spatula if the butter is too hot. Set aside.
Slide an oven rack into the center position, and preheat the oven to 375ºF (190ºC). Grease a 9-inch pie dish (or square pan) with olive oil. Set aside.
Bring a pot of water to boil and cook the large shell pasta over medium-high heat for 11 minutes. If you are using pasta of another shape, check the package for cooking times. Drain the pasta into a colander and rinse under cold water. Let the pasta finish draining as you prepare the cheese sauce.
Melt 1 tablespoon of butter in a large sauté pan or small pot over medium heat. Add the flour and whisk into the butter immediately, until a soft paste (or roux) forms. Let the paste cook about 30 seconds to 1 minute more, until it starts to bubble. Pour about 1/4 cup of milk and whisk it with the roux, until a thicker paste forms. Then pour the remainder of the milk.
Once the milk begins to boil, reduce the heat to medium low and simmer for another minute. Add the miso, oregano, thyme, black pepper, and salt and stir.
Add the butternut squash puree and mix until incorporated. Set aside a 1/4 cup each of the mozzarella cheese and white cheddar for topping the mac and cheese. Mix the remaining cheese with the butternut squash sauce. Turn off the heat.
Stir in the cooked pasta until the pasta is coated with the butternut squash cheese sauce.
Transfer the mac and cheese into the greased pie dish. Top with the reserved mozzarella and cheddar cheese. Spread the buttered rice cracker crumbs over the mac and cheese.
Bake the mac and cheese for 18 to 20 minutes, until the cheese around the edges of the pie dish is golden and bubbling.
Use oven mitts to take the pie dish out the oven and serve immediately. Serve the mac and cheese with a side of vegetables, like roasted asparagus.