Preheat the oven to 375°F (190°C). Grease a 9-inch pie dish with 1 tablespoon butter and press the pie crust into the dish. Prick the bottom of the crust several times with a fork.
Blind-bake the crust: Line the crust with parchment paper and fill with pie weights (or dried beans). Bake for 15 minutes. Remove the parchment and weights, then bake for 5 minutes more until the crust is just starting to turn light golden.
While the crust bakes, cook the bacon in a skillet over medium heat until crisp. Transfer to paper towels to drain, then crumble or chop.
In the same skillet, pour off excess bacon fat if needed, then add olive oil and 1 tablespoon butter. Add the sliced onions and cook over medium-low heat, stirring occasionally, until softened and golden (about 5–8 minutes).
Make the custard: In a large bowl, whisk together eggs, heavy cream, milk, salt, pepper, and nutmeg until smooth.
Assemble: Sprinkle the bacon, onions, Gruyère, and cheddar evenly over the warm crust. Slowly pour the custard over the fillings.
Bake for 35–40 minutes, until the edges are set and the center has a slight jiggle. If the crust is browning too quickly, loosely tent with foil near the end of baking.
Cool on a rack for at least 10–15 minutes before slicing. Serve warm or chilled.