Heat flax seeds in a 2-qt. saucepan over medium until toasted, 2–3 minutes; transfer to a bowl. Add quinoa to pan; heat over medium until toasted, 2–3 minutes. Add 1 cup plus 2 tbsp. water; boil. Reduce heat to medium-low; cook, covered, until water is absorbed and quinoa is tender, about 25 minutes. Stir in reserved flax seeds; let cool.
Whisk yeast, both flours, and salt in a bowl; transfer to a work surface and make a large well in the center. Whisk honey and 1½ cups water in a bowl and add to well; using your hands, slowly mix dry ingredients into honey mixture until a loose, sticky dough forms. Mix in reserved quinoa mixture and the raisins. Using your hands and a bench scraper to move dough, knead by pulling and folding dough up and onto itself, until puffed and airy, 4–5 minutes. Shape dough into a tight 6" round and drape a damp towel over top; let rest 4 hours.
Lightly dust dough with flour. Knead, by once again pulling and folding dough up and onto itself to incorporate air, until smooth and elastic, about 3 minutes. Shape dough into a tight 6" round; transfer to a lightly dusted baking sheet and chill 1 hour.
Arrange racks in lower and top third of oven; place a pizza stone on lower rack. Heat oven to 480°. Shape dough round into a 12"-long oval and pinch ends; transfer to a flour-dusted pizza peel. Lightly dust dough with flour. Use a razor or paring knife to slice a decorative leaf pattern into top of dough, cutting about ¼" deep. Use a pastry brush to brush dough with water. Slide dough onto pizza stone; bake until bottom of bread is golden brown, about 15 minutes. Transfer bread to upper rack; bake until bread is cooked through, 15–20 minutes more. Let bread cool completely before serving.