Heat oven to 400°F. Line a baking sheet with parchment paper. Cut squash in half and scoop out the seeds. Rub flesh with 1 tablespoon of the vegetable oil. Lay skin side-up on the baking sheet and roast until a fork easily goes through the squash, about 20-30 minutes. Remove from the oven and let cool.
Once cool enough to handle, scoop flesh out of the skin into a high powered blender or food processor. And blend until smooth.
Make the spiced squash butter: Combine 1/2 cup of the roasted squash, the 2 sticks of softened butter, 1 tablespoon brown sugar, 1 teaspoon ground cinnamon, and 1/4 teaspoon of kosher salt in a large bowl. Beat with a rubber spatula or wooden spoon until smooth and well combined. Set aside while you make the waffles.
For the waffles: Mix 1 1/4 cups all purpose flour, 1/3 cup ground flax seed, 1 tablespoon baking powder, 1 teaspoon kosher salt, and a 1/4 teaspoon each of the ground nutmeg, cinnamon, and allspice in a medium bowl.
Whisk 5 tablespoons brown sugar, 3/4 cup of the squash puree, 5 tablespoons oil, 2 eggs, 1 teaspoon vanilla and 1/2 cup of the almond milk in a separate large bowl until smooth and combined.
Mix in dry ingredients to make a thick batter, it's okay if it has a few lumps, don't over mix. Let batter sit 10 minutes while the waffle iron warms up.
Heat the waffle iron and once it is hot, spray both sides with cooking spray.
Spoon about 1/2 cup of the batter into the waffle iron and cook according to iron instructions. Serve hot with the spiced squash butter, maple syrup, and thinly sliced apples.