Primary reason: Larger packages are harder to lose while running the gauntlet of the various shipping carriers. Instead of buying the insurance offered by these carriers, just make the package large enough that only a bumbling idiot could lose it.

Supporting reason: It’s much cheaper and efficient. Factor in the costs of maintaining 500 assorted sizes of boxes on hand versus just 5. You have to organize, reorder, etc. And what happens when you discontinue that single product that was using the a box size that no other products use? Yeah, you eat those boxes. Also, I’d hazard a guess that the non-standard sized boxes cost alot more; just get 5 boxes that cover that the spectrum and that problem is effectively solved.

It’s a slightly absurd explantion :D, but the prevalence of such packaging is also an absurdity.