If you use a smaller ship with a smaller payload capability, you'll likely have to throw away at least the upper stage (as SpaceX does with their Falcon 9). By making both the booster and the upper stage huge, there is so much margin that you have enough fuel left over in the second stage to reenter and land after the mission. Throwing away stages is expensive. The largest cost for Starship launches will be the fuel - maybe a couple million dollars worth.