Preheat the oven to 400-degrees.
ROAST THE SQUASH: In a large bowl, toss the squash in the oil until well coated.
Season generously with salt and toss to combine.
Scatter the squash evenly onto a half sheet pan and bake until almost fork tender, for 10-15 minutes.
MAKE THE BAKED PENNE: Add the butter and sage leaves to a medium-sized saucepan.
Place over medium heat and cook until the butter is completely melted and begins to foam; remove from the heat and let sit for 5 to 10 minutes to infuse.
Bring a large pot of generously salted water to a boil.
Add the penne and cook for ⅔ of the recommended cooking time for al dente.
Meanwhile, finish the sauce; using a slotted spoon or cooking tweezers, remove the sage leaves, shaking off any butter, and discard.
Return the sauce pan to the stove and place over medium-high heat.
When the butter begins to foam, add the flour and whisk to combine, until completely incorporated.
Slowly drizzle in the milk, whisking constantly, until fully combined.
Cook, stirring often, until the sauce thickens and coats the back of a spoon, about 3 minutes.
Remove from the heat, add the nutmeg and pepper, and season with salt, to taste; whisk to combine.
Transfer the par-cooked pasta to a large bowl and add the sauce and stir to combine.
Add the roasted squash and fold until evenly dispersed.
Add ¾ of the mozzarella, and stir to combine.
Transfer to a 3-quart casserole dish and, using the back of a spoon or spatula, spread it into an even layer.
Sprinkle the remaining mozzarella evenly over the top.
Cover with foil, tenting it to keep it from sticking to the cheese, and bake for 30 minutes.
Remove the foil and bake until heated through and the cheese is golden brown, about 15 minutes.
Let rest for 5 minutes before serving.
Meanwhile, MAKE THE CRUMB TOPPING. In a small skillet, melt the butter over medium heat.
Add the garlic and salt and cook, stirring constantly, until fragrant, for 30 seconds to 1 minute.
Add the panko and cook, stirring constantly, until golden brown, about 5 minutes; transfer immediately to a bowl.
To serve, scoop the baked penne into a serving plate, sprinkle with the topping and some freshly grated pecorino; serve immediately.