The smoked red jalapeño, known as the chipotle chile, has gained such popularity that there's even a couple of cookbooks devoted to it! It particularly works well with barbecuing and grilling, both of which have considerable smoke associated with them.
Here's a pickled chile recipe from Tlaxcala. These sweet-hot pickled chiles can be the basis of a sauce of their own if they're further puréed, or they can be served as a condiment with enchiladas and other main dishes.
Note that this recipe requires advance preparation.
Why wouldn’t the cooks of Cerén have developed sauces to serve over meats and vegetables? After all, there is evidence that curry mixtures were in existence thousands of years ago in what is now India, and we have to assume that Native Americans experimented with all available ingredients. Perhaps this mole sauce was served over stewed duck meat, as ducks were one of the domesticated meat sources of the Cerén villagers.