Melt the butter in a medium saucepan over medium-high heat. Add the shallot and garlic and cook, stirring, until softened, about 2 minutes. Add the tomatoes and chipotle and cook, stirring, until slightly dried out, about 1 minute.
Add the cheeses and milk and heat at a bare simmer, stirring, until melted. Transfer to a bowl and serve immediately with your favorite dippers.