Are the bikes from eBay only semi assembled as well?
Unless the bicycle is child-sized, it would be
very difficult to get it into a bicycle box fully assembled. Bicycle boxes are designed to take bicycles with the wheel(s) off, handlebars off and turned, and pedals off at the very least. The wheels may very well have the skewers removed, and in some instances the rear derailleur might have to be removed or partially removed (if the bicycle is particularly large or the box is particularly small).
Edit: And the seatpost with saddle will likely be removed.
It's the same as what you'd do when you travel with a bicycle.