Those videos were mainly to show you how things can be done, and to give you ideas on how to mount boxes.
We know you're not likely to ever use such a big/complex setup, however it should give you ideas on how you could mount a single box, while making any fixtures as universal as possible.

If you look at the setup in the first videos, they use an extruded aluminium T-Slot bed to mount pneumatic clamps on. Using a T-Slot bed gives you easy adjustment, and the pneumatic clamps mean you get a wide clamping range so they don't have to be setup exactly. They just have to be setup to give enough clearance to get the boxes in, while making sure they clamp before running out of travel.
The pneumatics has the major advantage that a single valve controls the clamping of all the boxes.

To simplify that, use a T-slot base for the flexibility, and then use a two piece machine vice setup like magicniner has mentioned (first google hit - http://www.bison-bial.co.uk/vises/6522-200 to give you an idea of what we mean). Add in a block to the side of the vice to position the box prior to tightening, and you've got a repeatable setup for if you need to multiple runs.
With that kind of setup, you should be able to cover a very wide range of boxes.