Think about it on the macro level. They probably have a system in place, where if you use their "designated" boxes, it's super easy for them to throw it into an auto sorting machine and have a computer calculate exactly which shelf it'll go onto in a truck, which shelf and cargo hold on the plane, etc. They probably save a boatload of money using standard size boxes and envelopes and letting a computer figure out exactly how to cram the truck full of those boxes in the most efficient manner.
All "other" boxes probably get special attention from some human being who has to handle the box personally and make inefficient, human, sorting decisions on how to get this non-conforming box to its destination. Some idiot human (edit: idiot compared to a computer, not trying to diss USPS workers) being probably plays a lazy game of tetris with these boxes and there's probably a ton of gaps and inefficiencies on the trucks and planes that could've been utilized more efficiently by a computer that knows the exact dimensions of all the boxes its working with.
It doesn't matter if it's an "other" box that is the same size and shape as a "designated" box--even if it were EXACTLY the same size (and it would have to be EXACTLY, by the millimeter, I'm guessing) you would still need a human being to handle the box, measure it, determine it is EXACTLY the same, then mark it somehow to let the computer know that this "other" box should be treated the same way as Priority Box B4 or whatever.