Place the butternut squash in a microwave steamer basket. Add water to the bottom of the steamer and cook on high power for 5-7 minutes, until butternut squash is fork-tender.
Drain the steamer and toss the butternut squash and kale together. Place the lid on top of the steamer bowl and let the combination sit for 10 minutes to steam and wilt the kale.
Heat the olive oil in a large saucepan over medium heat. Add the garlic and cook until garlic begins to brown, stirring occasionally.
Lightly spoon flour into a dry measuring cup; level with a knife. Combine the flour and 1/2 cup of almond milk in a small bowl, stirring with a whisk until smooth. Add milk mixture and remaining 2 1/4 cups milk to garlic in hot saucepan; increase the heat to medium-high. Bring to a boil; cook 1 minute or until thickened, stirring often.
Remove from heat. Stir in 1 ounce each Cheddar -Gruyère and Parmigiano-Reggiano cheese, salt, and pepper; stir until cheese melts.
Coat baking dish with cooking spray. Spread 1/3 cup milk mixture on the bottom of the dish. Arrange 2 noodles over the milk mixture; top with half of the squash mixture and 2/3 cup milk mixture. Repeat layers once, ending with remaining noodles and remaining milk mixture. Cover with foil.
Bake for 15 minutes. Remove foil and sprinkle remaining Cheddar-Gruyère cheese and pecans over top.
Return to the oven and bake uncovered for 10 minutes or until lightly browned and sauce is bubbly. Let stand 5 minutes before serving.