Why sellers like flat rate
Flat-rate packaging can make pricing easier because the seller knows the service cost for a matching package and service. This can be useful for dense items that fit well.
When regular boxes may win
A regular right-sized box may cost less when the item is light, local, or does not fill the flat-rate package. It may also provide better presentation or cushioning space.
Planning rule
Flat rate is a pricing tool, not a universal packaging rule. Compare the packed item, not the empty box.