When standing on the measuring device, you would look straight down through the toes to the line on the measuring device. If you are measuring yourself, the number will face towards a fitter, and therefore will be upside down to you. This length is your foot length or true foot length. Once you determine your foot measurement, you still have to choose the correct shoe size. Shoes can run a full size short like a few import gym shoes.
Some shoes can run a half size short, like most gym shoes.
So you can have five different shoes with the same size on the box and they will fit five different lengths. The measurement of the foot, we call foot size. The way the shoe actually runs is referred to as true shoe size. As you have seen, box size is not true size. True shoe size is that size which still allows for one full size in front of the toes.