Add the almond flour, coconut flour, chipotle powder, salt, garlic powder, and xanthan gum to the bowl of a food processor. Pulse to combine.
Scatter the butter and the shredded cheese over top and process until the mixture forms a ball. Divide the dough in half and roll into logs about 1 ½ inches in diameter. Freeze the logs 1 to 2 hours, until firm but not rock solid.
Preheat the oven to 325F and line two baking sheets with silicone mats. Use a sharp knife to slice the logs ⅓ inch thick. Place the slices on the prepared baking sheets.
Bake 5 minutes, then remove from the oven and cover with parchment paper. Use a flat bottomed glass to press down and flatten each crisp to less than ¼ inch thick.
Bake another 15 to 20 minutes, rotating the pans halfway through baking. Bake until golden brown and just firm to the touch. Remove and sprinkle lightly with additional chipotle powder and some sea salt, if desired.