Rinse the brown rice and quinoa under cold water; drain well.
Warm 1½ tbsp olive oil in a medium pot over medium heat. Soften the onion with a pinch of salt, 3–4 minutes.
Stir in the garlic and brown rice. Toast until fragrant, about 1 minute.
Pour in the wine and let it simmer until mostly evaporated, about 1 minute.
Add 2¼ cups broth, ¾ tsp pepper, and 1 tsp salt. Bring to a boil, cover, and simmer 15 minutes.
Stir in quinoa and the remaining 1 cup broth. Cover and cook until grains are tender, 14–16 minutes.
Fold in peas. Cover off heat and steam 2–3 minutes. Fluff with lemon zest, lemon juice, parsley, and red pepper flakes.
While grains cook, season scallops with a little salt, remaining pepper, and smoked paprika.
Heat 1 tbsp olive oil and butter in a large skillet over medium-high. Sear scallops 1½–2 minutes per side until deep golden; work in batches.
Spoon pilaf onto plates. Sprinkle almonds, top with scallops, and drizzle any pan juices over the top.