I remember reading somewhere that the boxes are not sized to the items they contain, but to a combination of 'items they contain' and 'space we need the box to take up on the truck'; i.e. if you have five items of one unit size in a six-unit-wide truck they will slide around (and potentially get damaged, fall over, etc), but if you put one of those items in a two-unit-size box then the boxes will not slide around, meaning that while the box is inefficiently sized in isolation it is optimally sized in a logistical context.

I'm not sure how true this is, nor how reasonable it sounds since I don't know what the inside of an Amazon delivery truck looks like, but it sounds like the sort of thing that could be true in some circumstances.