I don't know the origin story of Pizza Box Guy, but it's a fully rigged 3d model that is set up as the default character when we start a new branch of our Buddha engine, which we call a "seed". If you look at the first days of the 3d Amnesia Fortnight games (Black Lake, White Birch, Autonomous, and Steed), you'll probably see PBG running around on day one or filling in for an enemy at the beginning of the project.
The cool thing about PBG is that we've done a bunch of placeholder animations for him - so he can walk, run, jump, attack, die, climb, etc, etc, and is a useful tool for prototyping.
I don't think we actually brought him fully rigged and animated into any of the unity prototypes - I remember we did load him up in Maya and squash and stretched some of his pizza boxes to play with different character proportions.
Ah - here it is!
Geoff used PBG to test proportions and early attack animations for Massive Chalice, before he was even in the game. So, Pizza Box Guy has proved useful for a bunch of things!
The method for creating a temp character like this is similar to that of any other character, you just don't need well-defined geometry and an advanced rig that has things like facial muscles. Maybe one of our character artists can hop on here and give more details.