Preheat oven to 400 degrees F. Line a baking sheet with parchment paper. Lay 16 slices bacon on prepared baking sheet and place in oven. Cook, turning once, until bacon is lightly crisped, about 12 minutes. Remove from oven and drain on a towel lined plate.
Line the wells of the muffin tin with remaining 12 slices bacon, pressing the bacon around the sides of the wells. Gently fold the corners of each slice of bread together and place the bread into the tin. Press the bread against the sides to make a well. Bake for 15 minutes.
Remove muffin tin from oven, place a slice of bacon in each piece of bread and break an egg on top. Sprinkle over about 1 teaspoon grated parmesan cheese and season with salt and pepper. Bake until eggs are set, about 13-15 minutes.
To finish, top one row of toast cups with a dollop of pesto and a sprinkle of parmesan cheese. Top another row with roasted red pepper and a pinch chili flakes. Top the third row with reserved 4 strips bacon, roughly chopped, and a sprinkle of chives.