Preheat the oven to 375 degrees F.
Roll out each pie dough into an 11 to 12-inch round on a clean dry surface. Cut 8 rounds from each disk using the biscuit or cookie cutter, re-rolling the scraps to create the last 1 to 2 circles if needed. Gently press the rounds into the bottom and up the sides of the muffin tins, and then pierce the bottom of the dough with a fork a few times to vent. Bake until the crust is set and slightly golden brown, 10 to 14 minutes. Let cool on a wire rack.
Bake the prosciutto on a sheet pan until crispy, 3 to 5 minutes. Once cooled enough to handle, break or chop into 1 to 2-inch pieces and reserve.
Melt the butter in a skillet over medium-high heat. Add the onions, olive oil, brown sugar, salt and crushed red pepper and cook, stirring often, until the onions are golden and tender, 6 to 8 minutes. Stir in the beet greens, dill, lemon zest and garlic and continue cooking until most of the liquid has been absorbed, 4 to 6 minutes. Remove from the heat and let cool to room temperature.
Whisk together the cream, sea salt, black pepper and eggs, and then fold in the Colby Jack, goat cheese and Parmesan.
Spoon a heaping tablespoon of the beet mixture into each crust, add a few pieces of prosciutto and pour the egg mixture on top. Place the muffin tins onto a baking sheet and bake until golden brown on top and still fluffy to the touch, 18 to 20 minutes. Let cool 5 minutes before gently transferring to a serving plate. Serve warm.