In a nonstick skillet, melt butter over medium heat. Add pumpkin seeds and stir to coat. Mix together cinnamon, chipotle, cumin, and salt, and sprinkle over pumpkin seeds. Stir well and cook for 2 minutes, until seeds start to get toasty.
Stir in honey, and continue to cook for 2 more minutes. Pour seeds out onto wax paper, parchment paper, or a Silpat liner, and let cool.
For the Pumpkin Muffins:
Preheat oven to 375° F. Coat muffin cups with cooking spray or fill with paper liners; set aside.
In a large bowl, whisk together flour, cinnamon, baking powder, salt, and baking soda.
In a medium bowl, whisk together pumpkin and sugar. Whisk in eggs, one at a time, then the milk, until well combined.
Pour pumpkin mixture into flour mixture. Stir briskly, with a spatula, until batter is combined. Do not overmix. Fill each muffin cup with about 1/3 cup of the batter. Sprinkle each with the spiced pumpkin seeds.
Bake until a toothpick inserted into the center of the muffins comes out clean, about 18 minutes. Remove muffins from tins while still warm.