Cook the sausage: In a large skillet over medium heat, cook the ground breakfast sausage, breaking it up, until browned and cooked through, 7 to 9 minutes. Drain and let cool slightly.
Prep: Preheat the oven to 400 degrees F. Grease a rimmed baking sheet really well or line it with parchment paper.
Mix the eggs: In a large bowl, whisk the eggs with the cottage cheese, garlic powder, salt, pepper, and chili flakes (if using). Stir in the diced scallions and cooked sausage.
Bake the eggs: Pour the egg mixture onto the prepared baking sheet and spread it evenly. Bake for 15-18 minutes, until the eggs are set and no longer jiggly. Let cool, then cut into 36 squares.
Toast the muffins: While the eggs bake, slice the English muffins in half and spread the cut sides with a little butter. Spread them out on a baking sheet and bake at 400 degrees F for 8 to 10 minutes, until lightly golden.
Assemble: On each muffin bottom, layer 2 egg squares and a slice of cheese, then close with the muffin top.
Wrap and store: Wrap each sandwich individually in parchment paper. Let cool completely, then store some in the fridge for the week and freeze the rest (see notes for freezer and reheating instructions).