Typically, when folks talk about "shippers", these are brown cardboard boxes with stamped and hand written info on the one end (like the bottom boxes in the OP's first picture) that Ruger places a firearm and the firearm holder box (think the yellow/black, red/black, red/white, newer white, gray plastic, etc. box like the middle boxes in the OP's first picture) into to protect the box and gun when they ship them out to whoever. When you ship a gun to Ruger, if/when they send you a box or when they return a repaired gun, it is typically in a generic brown cardboard box like the top box in the OP's first picture.
I am sure there are others that could/can explain even further about the shippers and their value and significance to a collector.