Preheat the oven to 350 degrees F. Grease a 9-by-13-inch casserole dish with softened butter or cooking spray and set aside.
Put corn, eggs, mayonnaise, butter, lime zest and juice, chipotle flakes, granulated sugar, brown sugar and 1 cup Cojita in the bowl of a food processor. Pulse in short bursts to break up the corn, about 1 minute, then process for 3 full minutes, stopping occasionally to scrape down the sides of the bowl with a silicone spatula. Add the flour, baking powder, salt, pepper and half the cilantro and again pulse in short bursts until just combined. Pour into the casserole dish, using the spatula to smooth, and bake uncovered until the pudding is barely set and a bit jiggly in the center, 40 to 45 minutes.
Just before the 40 minute mark, microwave the popcorn according to package directions, then empty the bag into a large bowl. Add the Tajin spice, remaining cilantro and 1/4 cup Cojita. Stir with a heavy wooden spoon or potato masher, roughly crushing the popcorn.
Top the pudding with the crushed popcorn, gently pressing it into the top with your hands (you may not use it all, depending on how thick of a popcorn crust you want). Sprinkle with the remaining 1/4 cup Cojita and return to the oven, 10 minutes more. Allow to rest for 10 to 15 minutes before serving.