The fuel indicator seems to be 1 to 2 gallons off, making my fuel tank capacity only 13 gallons. What can be done?

The fuel tank capacity never changes -- it is a physical amount of space that fuel will fill. It is what is stated in the owners manual -- likely the 15.9 gallons you have been told. You do not have a different size tank. Toyota would not just randomly mistakenly put a smaller tank in some vehicles. Please be aware that "distance to empty" readings are just an estimate based off of historical driving habits and information that is calculated by vehicle computer systems. It is not meant to be a factor by which someone runs the vehicle out of gas or depends on for safety's sake. You should always make an effort to fill your gas sooner than "7 miles to empty" if at all possible, even though in the real world it happens to all of us! Based on your calculations to the thousandths of a gallon of fuel, it is clear to me that there is a little bit of over-analyzing happening here. Are you resetting your miles per gallon average used every time you refuel? Make sure you do this, because your sample size can change each time. To sum up: it seems like your vehicle is operating as designed, consuming an appropriate amount of fuel, and indicating to you with relative accuracy the amount of fuel in the tank as well as can be measured by a sending unit: a float in the fuel tank that raises and lowers depending on the height of fuel in the fuel tank. To be clear: this is not a scientific measurement calibrated to fine tolerances. Finally: your Toyota dealer is the expert in this case. No one in this forum is going to have any kind of "better information" to dispel what you have been advised by the certified personnel who have been trained on the diagnosis and repair of your vehicle and the functionality of the vehicle.