I don't think it matters whether you can't pin it to just one site or not. Chocktaw, Muskogee and Cherokee populated different settlements and would have different capitals, none of which could be Cahokia, Moundville, Etowah or other cites in the area. Mound Building could however form the base of a Civ ability if you only plan on adding only one of the Mississipian successor civs, leaving no possible overlap. (and there's no reason to add more than one Southeast Amerindian civ) Similar to how Carthage's UA in CiV was "Phoenician Heritage" as there was no Phoenicia Proper that ability could clash with.