Melt butter in a skillet over low heat. Add onions, sprinkle with salt, and cook, stirring often, until onions are browned and caramelized, about 40 to 50 minutes. Sprinkle with pepper and remove from heat.

Sift the flours, baking powder, baking soda, and sugar into the bowl of a stand mixer fitted with the paddle attachment. Add kosher salt and mix for about 15 seconds.

Add butter pieces and pulse to start combining, then mix on low until butter is completely incorporated, about 3 minutes. If there are visible butter pieces remaining, break them up and mix in with your fingers.

With mixer on low, slowly add cream and crème fraîche. Mix until all ingredients are moistened and dough forms around the paddle, about 30 seconds.

Add onions and pulse until mixed.

Turn dough out onto a work surface, and, using the heel of your hand and a dough scraper, press the dough together and form a 7x9-inch rectangle. Wrap in plastic, and refrigerate for 2 hours.

Cut dough lengthwise to form two 9x3 1/2 inch strips, then cut each strip into 6 bars, each 3 1/2 x 1 1/2 inches in size. Place on a baking sheet lined with a silicone baking mat or parchment, wrap in plastic, and freeze at least 2 hours, preferably overnight.

(Once frozen, the scones can be placed in a plastic bag and kept frozen for a month.)

Preheat oven to 350°F. Place a rack in the center of the oven and line a baking sheet with parchment.

Arrange frozen scones on baking sheet, leaving about an inch of space between them. Brush with heavy cream and top with grated cheese and black pepper.

Bake 33 to 36 minutes, rotating front to back halfway through, or until scones are golden brown.

Let scones cool on the baking sheet before serving.