Whisk flour, salt, and spices in a bowl. Set aside.
In the bowl of a standing electric mixer, combine butter and brown sugar with the paddle attachment, beating until light and fluffy. Add honey and molasses and mix until fully incorporated.
Add the dry ingredients to the butter mixture in three additions, mixing until the dough comes together.
Form the dough into a flat disk, wrap tightly with plastic, and refrigerate for at least an hour (or up to two days) before continuing. Let the dough sit for a a few minutes at room temperature before rolling.
Preheat oven to 350º F. Lightly grease 12 cups in a standard-sized muffin tin.
On a generously floured surface, roll dough to a thickness between 1/8 and 1/4 inch. Using a 3¾-to 4-inch flower-shaped cookie cutter, stamp out 12 flowers (re-roll scraps if needed).
Gently transfer the dough to muffin tins, tucking each flower into one of the cups. With a toothpick or sharp skewer, prick holes in the dough around the bottom edge of the cup, about 1/8 to 1/4 inch apart, adding a few holes in the center as well.
Bake until the cookies feel just set, about 10 to 12 minutes.
Remove from oven and let cool in the muffin pans for about 5 minutes. Loosen the cups with a thin metal spatula before allowing them to cool completely in the muffin pans.