Set oven rack to middle position, and preheat oven to 425 °F. Arrange peppers on a parchment-lined rimmed baking sheet; roast for 20 minutes.
If using Italian sausage, heat olive oil in a 12-inch non-stick skillet over medium heat until shimmering. Add sausage; cook, breaking into small pieces with edge of spatula, until fully cooked and no pink remains. Transfer sausage to a paper towel–lined plate, and let cool.
Meanwhile, shred fontina and cheddar cheese on large holes of a box grater. In a large mixing bowl, toss cheeses, cornstarch, salt, granulated garlic, smoked paprika, nutmeg, thyme, oregano, and fennel seed until thoroughly combined. If using, mix in cooled sausage.
When ready, remove peppers from oven; lower oven temperature to 400 °F. Carefully cut a vent down the middle of top surface of each pepper. Make sure not to cut through bottom of pepper. Pull sides of the peppers open slightly to allow peppers to cool faster. When peppers are cool enough to handle, remove stems, cores and seeds. Open sides of peppers to lay flat on baking sheet. Divide cheese mixture evenly between peppers, piling mixture in middle of each pepper. Fold sides of peppers back towards middle, overlapping slightly, and press to seal.
Return peppers to oven for 20 minutes. Serve, garnished with balsamic reduction, fresh thyme, or grated parmesan.