So when you run the pkgutil step, it takes the DEST directory and makes a package, which you then have to run to actually install it in the correct location.

It's much more obvious in column view and cover flow. I didn't even realize it was there in icon view, too. They do seem to disappear once you set your icons smaller than a certain size.

Right, the first three versions would be 1x; 4, 4s, 5, 5s and 5c are all 2x. The two iPhone 6's are unknown in how you would classify them. Only the 6 Plus is big enough to be more than 3x the resolution of the original iPhone, but since apps for modern iOS versions don't run on the oldest iPhones, there's nothing to interpolate from the 1x resolution, so the point is moot.