WELLLLLLLLL....Some install scripts actually do just install the zkernel. They extract the boot.img, put it the file in, and repack it right there. I do it on a few of my roms, as it's kinda the easiest way to keep things updated (Same script I posted in the OP), and it's perfectly fine on most phones to do so.
What I (finally) figured out what was happening was that somehow I kept downloading files for the wrong variant of the GS3, (DERP) and it was writing to 05 instead of the 07 one.....Although, it still doesn't really explain why it would just full on brick it, but meh.