Make the crust: In the bowl of a food processor fitted with the steel blade, combine the almond and coconut flours, xanthan gum, and 1/2 teaspoon salt. Pulse a few times to combine. Add the butter and pulse until crumbly, 8 to 10 times.
In a small bowl, beat the egg, then whisk in the vinegar and pour the mixture onto the dough mixture. Pulse just until the dough begins to come together and resembles coarse, damp breadcrumbs, 3 to 4 times; do not over-process!
Scrape out the dough onto a large square of plastic wrap. Form the dough into a flat round about 6-inches in diameter. Wrap it tightly in the plastic wrap and refrigerate it for at least an hour.
Place the dough between 2 sheets of parchment paper. Working quickly to keep the dough cold, use a rolling pin to roll the dough between the parchment into a 10-inch circle. Patch any holes, tears, or cracks by pinching the dough together. If the dough becomes too soft and unmanageable, freeze it for 15 to 20 minutes, then try again.
Lift the dough using the parchment, then transfer it to a pie plate to cover. Decoratively crimp the edges around the plate, then prick the dough all over with a fork. Chill the prepared crust in the refrigerator 30 minutes or up to 1 day before filling and baking.
Parcook the crust: preheat the oven to 400°F (200°C). Place an oven rack in the center of the oven. Line the chilled pie crust with parchment paper and add enough dried beans or pie weights to fill the dish. Place the crust on a baking sheet and bake for 15 minutes. Remove the pie weights and parchment, tent the crust loosely with foil, and bake until dry, firm, and starting to slightly brown, about 15 minutes. Let cool.
Make the filling: In a medium skillet over medium heat, cook the bacon, flipping occasionally, until it’s lightly crisped, 10 to 12 minutes. Use a slotted spoon to remove the bacon to a plate. Add the shallots to the drippings in the pan. Cook, stirring frequently, until shallots are softened and lightly golden, 3 to 4 minutes. Remove to the plate with the bacon.
In a medium bowl, thoroughly whisk the cream and half and half with the eggs. Mix in nutmeg, 1 teaspoon salt and 1/4 teaspoon pepper.
Scatter the half of cheese, bacon and shallot into the par-baked pie crust. Transfer the crust to a baking sheet pan, pull the oven shelf halfway out and place the baking tray with the quiche. Pour in the egg and cream mixture right to the top and scatter the remaining grated cheese on top. Place a sheet of foil loosely over the quiche to prevent the edges from getting too dark.
Bake until a knife inserted 2 inches from the edge comes out clean, the center still has a slight jiggle and is not fully set, 40 to 50 minutes.
Remove to a wire rack and allow to cool for 10 minutes before serving.