Preheat oven to 350°F and grease an 8x8-inch baking dish.
Toss apples with brown sugar, lemon juice, cinnamon, nutmeg, gluten-free flour, and salt. Spread into dish.
Mix gluten-free flour, oats, brown sugar, cinnamon, and salt. Cut in cold butter until crumbly.
Sprinkle topping over apples.
Bake 40 to 50 minutes until golden and bubbling.
Warm milk for custard.
Whisk egg yolks, sugar, cornstarch, and salt.
Slowly whisk warm milk into egg mixture.
Return to saucepan and cook on low, whisking, until thickened.
Stir in vanilla and serve warm over crumble.