Heat oven to 425 F.
Heat 1 tablespoon olive oil over medium-low heat. Add the onions and a pinch of salt and stir to coat. Cook, stirring occasionally, until well-browned and caramelized, about 45 minutes.
Stir in the garlic and sauté until golden and fragrant, 2 minutes. Remove pan from the heat.
In a medium bowl, toss together the butternut squash, 2 teaspoons olive oil, thyme, rosemary and sage. Season with salt and black pepper.
Transfer the squash to a rimmed baking sheet lined with parchment paper and roast, turning halfway through, until just fork-tender, 30 to 35 minutes.
Place the pizza crusts side by side on a large baking sheet. Spread the caramelized onions over the crust, leaving a ½-inch-thick border around the edges. Divide and scatter the goat cheese on top.
Slice the fresh mozzarella into 8 ¼-inch-thick circles. Using a small cookie cutter or a paring knife, cut each slice into the shape of a ghost. Place 4 ghosts on each pizza. Place 2 pepitas on each ghost to create eyes.
Divide and scatter the remaining pepitas and butternut squash all over the pizzas, leaving the ghosts uncovered.
Transfer the pizzas to the oven and bake until the mozzarella is melted and the crusts are golden brown, 12 to 15 minutes.
In a small bowl, toss together the kale, apple cider vinegar and remaining 1 teaspoon olive oil. Scatter the kale onto the pizzas and around the ghosts. Serve hot.