Preheat the oven to 375°F and line a 12-cup muffin tin with paper liners.
Toss the diced apples with 1 tablespoon of flour so the pieces stay suspended in the batter instead of sinking. In a small bowl, mix the sugar and cinnamon for the topping.
In a large bowl, whisk together the remaining 2 cups flour, baking powder, baking soda, salt, cinnamon and nutmeg.
Blend the cottage cheese, eggs, brown sugar, granulated sugar, melted butter and vanilla until smooth, 30-45 seconds.
Fold the wet mixture into the dry ingredients until almost combined, then fold in the apples and caramel bits.
Divide the batter among the cups, filling them to the top, and sprinkle with the cinnamon sugar.
Bake for 22-25 minutes, until golden and a toothpick inserted into the cake part comes out clean.
Cool for 15 minutes. Warm the caramel sauce slightly, drizzle over the muffins and finish with a pinch of flaky sea salt.