Preheat your oven to 350°F. Grease the wells of a 24-well miniature muffin tin and set it aside.
Make the filling.
In a medium-size bowl, place the cream cheese, sugar, and salt, and beat with a handheld mixer (or a whisk, vigorously) until light and fluffy. Add the egg yolk and whisk by hand until just combined. Cover the filling and set it aside.
Make the cookie dough.
In a large bowl, place the flour, xanthan gum, baking powder, salt, and granulated sugar, and whisk to combine well. Add the brown sugar and mix, breaking up any lumps.
Create a well in the center of the dry ingredients, and add the butter, honey, molasses, vanilla, and egg yolks, and mix to combine.
The dough should come together and be thick but soft. If necessary to bring the cookie dough together cohesively, knead in some lukewarm water by the half teaspoonful.
Shape & fill the cookie dough.
Scoop the dough into portions about 2 teaspoonfuls each, roll each mound of dough into a ball between your palms, and place in the center of each of the prepared wells of the miniature muffin tin.
With a clean index finger, press a hole into the center of each ball of dough. Using your index finger and thumb, pinch the dough to thin the sides and press them toward the edges and bottom of the muffin well.
Using a small spring-loaded ice cream scoop or two spoons, fill each of the wells about 3/4 of the way full with the cheesecake filling.
Repeat with the remaining balls of dough and cheesecake filling. You will need to repeat the process with about 6 more wells of the muffin tin in a second round.
Bake the cookies.
Place the muffin tin in the center of the preheated oven and bake until the cookie cups are just beginning to brown around the edges and the filling is mostly set (about 12 minutes). Do not overbake.
Remove from the oven and allow to cool on the baking sheet for at least 10 minutes or until firm.
To remove the cookie cups from the muffin tin, twist them in the wells to loosen them, then pry them out with a toothpick inserted gently on the side of the cookie cups.
Chill the cookie cups until the filling is firm, about 1 hour. Drizzle lightly with melted chocolate, if desired.
These cookies can be frozen in a single layer on a rimmed baking sheet, then piled into a freezer-safe zip-top bag for longer storage.