Making a custom box can be used for a few good reasons that I have found, as well as- I'm sure it could be used for various other and different reasons. Maybe it is a holiday season and you are wrapping a gift that needs a box for shape or structure; or would benefit from a layer of protecting cardboard; or need to fit an item of an odd shape/size into a box for storing/mailing.
I make boxes for the items that I sell on eBay. Making an item's own box minimizes the size, the weight, the need for more packaging material, and thus making the postage/shipping fees less.
All you need is second hand cardboard, a box cutter (razor blade), and packing tape (in a dispenser works best).