For the pineapple: Preheat the oven to 450 degrees F. Grease a 12-cup muffin pan with cooking spray.
Combine the brown sugar, butter, allspice, kosher salt and cinnamon in a skillet over medium-low heat and cook until bubbling. Add the pineapple, stir to coat and cook until the liquid has nearly evaporated and the caramel has deepened in color, about 7 minutes.
For the muffins: Meanwhile, working quickly, whisk the boiling water into the cornmeal in a large bowl until you get a stiff mash. Whisk in the buttermilk, stirring until smooth. Stir in the egg, then add the flour, granulated sugar, baking powder, kosher salt and baking soda and mix until just incorporated.
Add 2 to 3 pieces of the pineapple to the bottom of each muffin cup. Evenly divide the cornbread mixture among the muffin cups, filling each three-quarters of the way full.
Bake for 15 minutes. Cool on a wire rack for 5 minutes. Use a paring knife to remove each muffin, flipping it to reveal the caramelized pineapple before placing on a plate. Sprinkle with flaky sea salt and serve!