Through some unknown Pepakura magic, clicking "unfold" and "save as" can automatically reduce the file size down to about 1/3 of the original .pdo so I'm not sure how it was originally saved or why doing this reduces it so much.
The other thing I do is I import the .obj (either the .obj file provided, or just exported from the .pdo file) into Maya and reduce polygons, move vertices, simplify geometry, and move some of the overlapping edges that would interfere with foam building. The original torso has upwards of 25,000 polygons, and the combined total of the chest and back after editing is just over 11,000 which makes unfolding and building much more simple. I wish the model was clean enough that it could just be unfolded directly.
I'm editing the helmet right now, but not reducing the poly count as much, just because it'll be important to keep as much detail as possible.It'll just mostly be removing inside layers and adjusting some of the angles that are too complex for foam.