Preheat oven to 350 degrees. Toast almonds until crisp, lightly browned, and fragrant, about 7 minutes. Remove from oven and set aside. Meanwhile, place quinoa in a fine sieve and rinse under cold running water until the water runs clear; drain well.
In a medium saucepan, heat 2 teaspoons olive oil over medium heat. Add yellow pepper, garlic, scallions, and red-pepper flakes; cook until the pepper is crisp-tender, about 5 minutes.
Stir in quinoa, thyme, 1 cup water, and 1/4 teaspoon salt. Bring to a boil, reduce to a simmer, cover, and cook 7 minutes. Stir in zucchini, cover, and cook until quinoa is tender but not mushy, 5 to 8 minutes longer. Remove the saucepan from heat.
Stir in celery, almonds, and remaining 2 teaspoons oil, season with salt, and fluff with a fork. Cool to room temperature before packing into two containers and refrigerating. When ready to eat, squeeze lime over salad, if desired. Serve with additional lime wedge and thyme, if desired.