Preheat the oven to 400F. Line a baking sheet with parchment paper.
Arrange acorn squash slices on the prepared baking sheet then coat with one tablespoon of olive oil, ground nutmeg, and a healthy pinch of salt and pepper. Toss to coat then roast in the oven until tender, about 20-25 minutes.
Meanwhile, heat the remaining tablespoon of olive oil in a small-ish skillet over medium heat. Once oil is hot, add the diced pancetta, minced shallot, minced garlic, ground sage, and a healthy pinch of salt and pepper. Toss to mix up then sauté until pancetta is crispy and shallots/garlic are very fragrant, about 10 minutes, stirring occasionally.
Spread 3 tablespoons of whipped cream cheese on each flatbread, leaving a ½-inch border sauce-less as crust. Top the whipped cream cheese with thinly sliced apples, roasted acorn squash, then the crispy pancetta/shallot mixture. Finally sprinkle goat cheese and shredded mozzarella over top of both flatbreads.
Bake flatbreads in the oven until the cheese is melted and the crust is golden, about 10-13 minutes. Remove from the oven, drizzle honey over top, then slice and serve!