Preheat the Oven: Preheat your oven to 400°F (200°C). Line a rimmed baking sheet with parchment paper or a silicone mat.
Prep and Roast the Squash: Cut the butternut squash into ½ inch cubes. Place the squash on the prepared baking sheet, drizzle with olive oil, and sprinkle with a pinch of salt. Roast in the preheated oven for 30 minutes until tender. Once done, let the squash cool for a few minutes. Reduce the oven temperature to 350°F (175°C).
Make the Cashew Ricotta: While the squash is roasting, prepare the vegan ricotta (using cashews or tofu) and mix in the spinach. Set aside.
Cook the Pasta: Cook the jumbo pasta shells according to the package directions. Drain and set aside.
Make the Butternut Squash Sauce: In a food processor or high-speed blender, add 4 cups of the roasted butternut squash, reserving the rest to stuff the shells. Add the garlic, red pepper flakes, thyme, salt, and 1 cup of water or vegetable broth. Blend until smooth, adding more liquid as needed to achieve a sauce-like consistency (about 1½ cups in total). The sauce should be thick but pourable.
Layer and Stuff the Shells: Spread a layer of the butternut squash sauce across the bottom of a 12-inch round or 9×13-inch rectangular baking dish. Scoop one heaped tablespoon of ricotta filling into each cooked shell, along with 3 pieces of roasted butternut squash. Arrange the stuffed shells in the baking dish.
Bake: Cover the dish with foil and bake in the preheated oven at 350°F (175°C) for 15-20 minutes, or until the shells are warmed through.