Melt butter in a medium saucepan over medium heat. Cook onion, chile, jalapeños, and garlic, stirring, until tender but not browned, 8–10 minutes. Add tomatoes, season with salt, and continue to cook until juices have evaporated, about 6 minutes. Stir in flour and cook until incorporated, about 1 minute. Whisk in milk and continue to cook until mixture comes to a boil and thickens, about 4 minutes. Reduce heat to low, gradually add both cheeses, and cook, stirring constantly, until cheese is completely melted and queso is smooth. If it seems too thick, stir in a little more milk.