Heat a comal or a dry skillet over medium-high heat. Rinse the poblano peppers and red bell pepper thoroughly, then pierce each with a knife to allow steam to escape. Place the peppers on the comal and roast, turning as needed until the skins are evenly blistered and blackened on all sides. Once roasted, transfer the peppers to a plastic bag, seal, and cover with a kitchen towel. Let them steam until cool enough to handle. Then, gently rub off the blackened skins. Carefully slit each poblano pepper on one side to remove the seeds while keeping the stems intact. Set the peeled and seeded poblano peppers aside for stuffing in later steps. Chop the peeled, deseeded red bell pepper.
Heat a large skillet over medium-high heat and add the olive oil. Sprinkle the chopped shrimp with 1/4 teaspoon salt, then add them to the hot skillet. Cook for about 3 minutes, stirring occasionally, until the shrimp is pink and just cooked through. Remove the shrimp from the pan and set aside for use in the filling.
Using the same skillet over medium heat, add the minced garlic and sauté for about 30 seconds, stirring constantly. Sprinkle in the flour and ground red pepper, and cook for 1 minute, stirring continuously to form a roux. Gradually whisk in the crema Mexicana (or sour cream) and 1/2 cup of the milk, stirring to combine. Let the sauce cook for 1 minute until slightly thickened. Remove from heat, let it stand for 2 minutes, then add the shredded quesadilla cheese and the remaining 1/4 teaspoon salt. Stir until the cheese is melted and the sauce is smooth—I like to take my time here to make sure the cheese melts completely, which gives the sauce a luxurious texture.
In a large bowl, combine 1/3 cup of the cheese sauce from Step 3 with the chopped roasted red bell pepper (from Step 1), cooked shrimp (from Step 2), chopped cilantro, and fresh lime juice. Toss everything together until evenly coated to form the filling. Stir the remaining 1/4 cup milk into the reserved cheese sauce to thin it slightly and keep it warm for serving.
To serve, spoon about 3 tablespoons of the reserved cheese sauce (thinned with milk) onto each plate. Gently stuff each prepared poblano pepper (from Step 1) with 6 tablespoons of the shrimp filling (from Step 4). Place two stuffed poblanos on each plate over the cheese sauce. Garnish with crumbled queso fresco, extra cilantro sprigs, and, if desired, pomegranate seeds for a festive touch.