A box fee is certainly an industry standard among wholesale and retail operations. I use to manage a couple small LFS and we were always charged a box fee as well as for any heat packs or cold packs when we ordered livestock shipments. Many online retailers follow this model also and charge a box fee as well as for heat packs, etc. If a retailer doesn't charge this fee, you are still paying it somewhere along the line. It may be in higher prices for the livestock. So shippers could have higher livestock prices and free boxes or lower livestock prices and charge a box fee. Bottom line is it is an operating expense and the consumer pays for it one way or another.
Now as far as a private seller.... That is a little different I think. If I were going to sell someone something and ship it, I would disclose the shipping and handling (box fee included) up front. Nothing wrong with charging for it, but it should be disclosed at the time of purchase. I guess it is REALLY important to ask as well. Of course if I had extra boxes that I obtained for free I wouldn't charge a box fee, but that is just me.
It is the shipping cost and box fees that CAN make LFS a better deal even though their prices on the items are much higher. At the LFS the shipping, handling, box fee, etc are already built into the final sale price. Online you might find a coral for $19.95, but shipped that coral could easily cost $50-60. The same coral might sell for $39.99 at a LFS. Which is the better deal? Of course when you buy in quanity it is a different story. If you have a reef club or something like that you can make larger orders online and save BIG bucks. Just depends I buy different things in different ways.