Preheat oven to 400 degrees F (200 degrees C). Grease 2 baking sheets.
Stir flour, flax seeds, chia seeds, baking powder, salt, garlic powder, onion powder, and dried chipotle pepper powder together in a large bowl. Cut butter into flour mixture with a pastry cutter until mixture resembles coarse crumbs.
Stir water and olive oil into butter-flour mixture with a fork until dough sticks together and pulls easily off the sides of the bowl. Divide dough into 2 portions.
Turn 1 dough portion out onto a floured work surface and roll out as thin as possible. Cut dough into squares and place on prepared baking sheet. Repeat with remaining dough.
Bake in the preheated oven until crackers are golden and crispy, about 8 minutes. Transfer to a wire rack to cool completely.