It's not low quality cheese. It's the wrong cheese. Pizza Hut, PJ's, and Donato's all used string cheese in their stuffed crust when I worked there. Domino's didn't do stuffed crust when I worked there.

String cheese is certainly easier to deal with, but that is pure mozzarella, not the usual mozzarella romano blend that most pizza places use. I dunno what the moisture of string cheese is either, but the shreds/cubes of the normal stuff was all marked "low moisture blend." I suspect that string cheese is more wet of a mozzarella, and it would be a better, but harder to assemble product if they just used the normal stuff.