Cook the macaroni according to the package instructions. Don't overcook it. It should be tender, but firm (5-8 minutes).
Drain the macaroni and transfer it to a large bowl.
Place the squash and milk in a large saucepan and cook over medium heat. Stir occasionally and bring to a boil.
Transfer to a blender or food processor and combine until smooth.
Transfer back to saucepan and stir with grated soft cheese and ricotta until the cheeses are all melted.
Remove from heat and add salt, mustard, and cayenne pepper.
Pour cheese mixture over the macaroni and stir to combine.
Mix in the garlic and onions.
Fill cupcake liners with the mixture. Because this is mac and cheese and not cupcake batter, you don't need to worry about the mixture rising. Don't be afraid to fill the liners in a heaping mound. The mac and cheese cupcakes will look more fun that way.
In a small bowl, combine grated hard cheese, panko breadcrumbs, and oil.
Sprinkle mixture over the top of the mac and cheese cupcakes.
Bake at 375 F for 20 minutes or until topping is lightly browned.