In the bowl of a stand mixer fitted with a dough hook, combine the all-purpose einkorn flour, spelt flour, and salt.
In a separate bowl, whisk together the warm milk, melted butter, sugar, egg, and egg yolk until well combined.
Stir in the sourdough discard until incorporated.
With the mixer on low speed, gradually pour the wet mixture into the flour mixture and mix until a shaggy dough forms with no dry flour remaining.
Increase the speed to medium-low and knead for 8 to 10 minutes, until the dough becomes smooth and elastic. Add extra flour a tablespoon at a time if needed.
Transfer the dough to a clean bowl, cover, let it rise at room temperature for 1 hour, then refrigerate overnight.
To make the filling, beat the cream cheese, sugar, flour, vanilla, and salt on low speed until smooth.
Add 1 teaspoon lemon juice, mix, and adjust to taste if needed. Cover and refrigerate.
To make the streusel, combine the flour, sugar, and chilled butter in a small bowl. Rub together with your fingers until the mixture resembles wet sand. Cover and refrigerate.
The next day, remove the dough from the refrigerator, punch it down, and place it on a lightly floured surface.
Line a rimmed baking sheet with parchment paper.
Shape the dough into a 9-inch log and cut into 9 equal pieces.
Form each piece into a ball, pinching the edges underneath and rounding the surface until smooth and taut.
Arrange the dough balls seam side down on the baking sheet, spacing them about 1 1/2 inches apart.
Cover and let rise for 2 to 3 hours, until increased in size by about half.
Preheat the oven to 350°F.
Grease the bottom of a 1/3-cup measuring cup with butter and dust lightly with flour.
Press firmly into the center of each dough ball to create an indentation.
Spoon about 1 1/2 tablespoons of filling into each indentation and smooth the tops.
Whisk the leftover egg white with a little water and brush the edges of the dough.
Sprinkle streusel over the edges, keeping it mostly off the filling.
Bake the Healthy Sourdough Discard Kolaches for 20 to 25 minutes, rotating the pan halfway through, until golden brown.
Cool on a wire rack for about 20 minutes before serving.