I work in games, and this is actually not true. The various foot gear we have vary widely in size of the foot and height (take a look at that one foot gear from pvp that resemble hoofs). The foot/shoe models are created with a variance on where the foot starts and stops, without changing our character's height;
http://s21.postimg.org/yqq9316h3/feet.png
These pictures were taken from the same camera angle, yet look at the difference in height from the base of the feet and the ground (if i had a choice as the the modeler, i'd use the ninja kyahan as a base to create a bare-foot "boot").
There isn't anything tech-wise preventing SE from creating a bare-foot look. It's as easy as creating a new boot. The only thing that stops them from doing so is... well they just don't want to.