Position the oven rack in the upper 1/3 position. Preheat the oven to 425° F.
Place the ball of pizza dough on a lightly oiled quarter sheet pan. Roll out (it doesn't need to reach the edges of the pan, it will expand). Cover with plastic wrap and let rest in a warm area.
On a baking sheet, toss together the olive oil, butternut squash, honey, sage, cinnamon, cayenne, and a pinch each of crushed red pepper flakes, salt, and pepper. Roast for 15-20 minutes, until the squash is just tender and remove from oven. Increase the heat to 500° F.
Meanwhile, caramelize the onions. Melt the butter in a large skillet over medium-high heat. Add the onions and cook 3 minutes, until softened. Add half the apple cider, season with salt and pepper and continue cooking another 5 minutes, until the cider has mostly evaporated. Add the remaining cider and cook another 5 minutes or until the onions are golden and caramelized. Add a pinch of crushed red pepper, cook another minute. Remove from the heat.
To assemble. Remove the plastic wrap. Gently press the dough until it covers the entire sheet pan. Top with the onions, you may not need them all. Add the cheese, then the prosciutto. Then arrange the butternut squash on top.
Slide into the preheated 500° F oven and bake for 10 minutes, rotate the pizza, and bake another 3-5 minutes or until the crust is golden and the cheese has melted. Top the pizza additional crushed red pepper flakes, a drizzle of honey, and a sprinkle of sea salt.