Pour the honey into a small saucepan. Bring to a simmer over medium heat. Turn off the heat, add the habanero, then allow the honey to cool to room temperature.
Strain through a fine-mesh sieve into an airtight container. Set aside.
Baked Beans
Heat the olive oil in a pot over medium heat. Add the onions and cook until translucent, 3-5 minutes.
Add the beans, brown sugar, bacon, port, molasses, 1 tablespoon of the habanero honey, chili powder and salt. Stir to combine, and bring to a simmer over medium heat. Reduce the heat to medium-low and simmer gently until the mixture is reduced by half, about 20 minutes.
Turn off the heat and set aside to cool to room temperature.
Mini Bacon Cups
Preheat the oven to 350 degrees.
Turn a mini muffin pan upside-down and lightly coat the bottom with nonstick pan spray. Crisscross 3 pieces of bacon over each upturned cup, and then place another mini muffin pan on top so that the bacon pieces are compressed between the two pans.
Place the pans on a rimmed baking sheet and bake until the bacon cups are crisp and browned, about 20 minutes.
Remove the baking sheet from the oven and set aside to cool completely. Lift off the top pan. Carefully remove the bacon cups from the bottom pan and place them on a paper-towel-lined baking sheet to drain, wrong side up.
To Serve
Gently reheat the beans in a saucepan over medium heat until warmed through (add 1 tablespoon water if they’re too thick or dry).
Place a spoonful of the beans into each bacon cup. Serve.