Those 100 yen machines are rare. I lived in Kyoto, and can recall seeing only one in the city. People would go out of their way to use it. More typically, you will see machines that have 120円 prices by reducing sizes. Buy the same drink in the conbini next door, and you’d get twice the volume.

Regardless, if you’re in a place where vending machine prices are lower than usual, it only means that the store prices are lower still. There’s no magic here; the vending machine operators are making a healthy profit.