The nice thing about an IR touch screen is that the emitters/receivers sit around the edge of the screen. Since everything is contained in the bezel, it does not interfere with the display itself.

EDIT: it is also worth noting that phones and tablets do have recessed screens. The difference is that there is a glass or plastic surface over the screen. That may offer a flush surface as far as our hands are concerned, but it interferes with the display itself. In the case of phones and tablets, most people don't care about that interference. In the case of ereaders, people do care.