Preheat your oven to 400F (200C). Lightly grease a pizza pan.
Add the squash cubes, onion, olive oil, garlic, salt, and nutmeg to a large bowl and toss to coat evenly. Dump onto a baking sheet and spread into one even layer. Bake for 30 minutes, flipping halfway through until fork tender. Remove from the oven and turn the oven up to 450F (230C).
Remove from the oven and add to a blender or food processor. Pour in the non-dairy milk, and blend on low to combine into a creamy sauce, stopping to scrape down the sides as needed.
Lightly flour a clean work surface. Stretch the pizza dough to fit the pizza pan. Spread a nice thick layer of the squash sauce on your pizza, then sprinkle with sage leaves. Add a few cracks of pepper. Bake for 15-20 minutes, and bake until the crust is golden. Serve hot or cold.