Since you're working with very hot sugar syrup, you do need to be careful when mixing the caramel with the popped corn. I would highly recommend using a thermometer since the caramel goes from the proper temperature to burnt in a flash.
If you want to make this even more decadent, melt about 5 ounces of bittersweet chocolate and drizzle over the top of half the caramel corn once it's cooled. Place the baking sheet into the refrigerator to set the chocolate.
Preheat the oven to 250 degrees. Set the racks to the middle and upper 1/3 of the oven. Coat a large roasting pan with non-stick spray. Line 2 baking sheets with parchment paper and coat the parchment with non-stick spray. You'll also want to coat a large rubber spatula with the non-stick spray.
Mix the salt and chipotle powder together in a small bowl and set aside. Pour the oil into a 4-quart pot set over medium heat. Once hot, add the popcorn kernels and cover with a tight fitting lid. Shake the pot occasionally as the corn is popping and once the last kernel pops, remove the pot from the heat. Dump the popped corn into a large mixing bowl and immediately sprinkle on the salt and chipotle mixture. Toss to coat, then mix in the almonds and pepitas.
Wash and dry the 4-quart pot. Add the sugar, water, and corn syrup. Stir to combine, then with a pastry brush dipped in water, wash down the sides of the pot to get rid of any sugar crystals that may have stuck to the sides of the pot. Clip the thermometer to the side of the pot and place the pot over medium-high heat. During the cooking process, you'll need to wash down the sides of the pot with the pastry brush several times to keep the sugar from crystalizing. Don't stir the sugar. Bring the sugar to the caramel stage (320 degrees), which takes about 18 minutes. The sugar will be a deep amber color.
Just before the sugar reaches the caramel stage, scrape the popped corn and nuts into the prepared roasting pan. As soon as the sugar reaches 320, pour it over the popped corn and using the coated spatula, stir to evenly coat the popped corn and nuts. Divide the mixture between the two baking sheets, spreading into an even layer. Place the sheets into oven and bake for 30 minutes, switching the baking sheets halfway through the baking time. Remove from the oven and let cool completely. Place into an airtight container to store.