It's my understanding currently that a 'production' starship will have three central engines optimized for sea level, and additionally three vacuum-optimized engines installed around its inside base perimeter.
Indeed. Those engines are currently missing partially because there's no reason to lose more engines than strictly necessary and also because they only need that much thrust when the fuel tanks are completely full.
If they decide to lift the StarShip from sea level completely full they will need to use only sea level engines (not vacuum optimized) or risk engine damage. Of course in production the booster will put the StarShip (upper stage) well above sea level.
