In a large bowl, whisk together the gluten free flour, tapioca starch, instant yeast, sugar, xanthan gum, and salt. Add the warm milk, eggs, melted butter, and apple cider vinegar. Stir until a soft, sticky dough forms.Cover the bowl with plastic wrap and let the dough rise in a warm place for about 1 hour, until it has doubled in size.
Line a large baking sheet with parchment paper. With well-oiled hands, divide the dough into 8 equal portions. Flatten each portion into an oval shape about 1/2 inch thick and roughly 4 inches long.
Place a sausage link and a half slice of cheddar cheese in the center of each oval. If using jalapenos, add a few slices on top of the cheese. Wrap the dough up and around the filling, pinching the seams together on the underside.Place each kolache seam-side down on the prepared baking sheet, spacing them about 2 inches apart.
Cover the kolaches loosely with a kitchen towel and let them rise for 30 to 40 minutes, until noticeably puffy.
Preheat the oven to 375 degrees F. Bake the kolaches for 18 to 22 minutes, until golden brown on top and the dough is cooked through.
Remove from the oven and immediately brush the tops with melted butter and sprinkle with flaky sea salt. Let cool for 5 minutes on the baking sheet before serving warm.