Heat oil in a large, heavy-bottomed saucepan over medium heat. Cook onion, bell peppers, and fresh chiles, stirring often, until softened, about 5 minutes. Add flour and stir until peppers are coated and flour is yellow, about 1 minute.
Add milk, stirring constantly until incorporated, then add 3/4 cup water, stirring constantly until thickened and hot (the mixture will look pasty at first).
Sprinkle in half the cheeses, stirring until melted and smooth. Repeat with remaining cheeses. Add chipotle chiles and their sauce and salt and mix until blended. Serve with tortilla chips.
Make ahead: Up to 2 days, chilled. Bake at 400°, covered, stirring once, until warm and smooth, about 20 minutes.
Note: Nutritional analysis is per 1/4-cup serving.