Your comments

Agreed, but we need to change the way we store projects. So maybe we'll done this in version 5.
As long as Boxshot keeps references to external shapes instead of storing them inside the projects, adding files to the left panel means that the project will not open on another computer.

That's why we recommend to manage external 3D files manually, exactly as you manage texture images.

We'll probably change this in the future versions of Boxshot and then you will be able to add shapes to the left panel.
You can still export the shape to Boxshot and assign the inside there.
You can use custom color bar images to do so. Please provide some examples of the result you need, so we can better understand the idea.
Imposition Wizard has shuffle option that allows you to reorder pages before imposing them. Isn't that enough? Could you provide some before/after samples?
IW got a "shuffle" mode that allows you to rearrange and flip the pages you need. Isn't it what you want?