Combine apple and 1/4 cup water in a small skillet; bring to a boil. Stir in cinnamon, nutmeg, and cloves; cover, reduce heat, and simmer 4 minutes or just until crisp-tender. Remove from heat; uncover and let stand.
Bring 2 cups water to a boil in a large saucepan over high heat; stir in quinoa flakes and salt. Cook 1 1/2 minutes, stirring frequently. Remove from heat; stir in sugar, and let stand 5 minutes or until slightly thickened.
While cereal stands, return apple mixture to medium heat; add syrup, butter, and vanilla, stirring just until butter melts. Serve apple mixture over cereal.