Heat oil in a 10-inch skillet until hot. Cook tortilla strips in the hot oil until they are light golden brown, about 30 to 60 seconds; drain on paper towels and set aside.
Cook onions in margarine in a 3-quart sauce pan over low heat until tender, then stir in the flour, salt, pepper, and cumin.
Cook, stirring constantly, until mixture is bubbly. Remove from heat; stir in half and half. Return to the heat and bring to a boil, stirring constantly. Boil and stir for 1 minute, then reduce the heat to low.
Stir in the chipotle chile, scallops, and shrimp. Cook over medium heat, stirring frequently, just until the shrimp are pink, about 9 minutes.
Layer half of the tortilla strips in the bottom of a greased 3-quart casserole or large heavy ovenproof skillet; top with half of the seafood mixture. Repeat with the remaining tortilla strips and seafood mixture. Top with the bacon.
Bake in the preheated oven until hot, 15 to 20 minutes. Top with cheese and return it to the oven until the cheese is melted, about 5 minutes.