Your comments

Will it be enough to rotate the output sheets instead?
You can use snapshots for that in Boxshot. If you mean Origami, the workflow assumes export to Boxshot for further scene composition and rendering.
Images can be imported by dragging and dropping them onto the shape. There is a quick start guide at the "Welcome" screen that shows the process as a series of slides, please have a look to get the basics.
You could add your own graphics as a color bar, by adding it next to the standard ones, or simply dragging them into the Inspector window of the Standalone version. Does it help, or you need to replace the start target/bull eye ones?
We suggest to use custom colobars for that. Imposition Wizard can place a colorbar to any part of the sheet and you can load your own colorbar art, so that's the way to put a custom mark wherever you want.
This has been added in version 2.5, the feature is called "backside offset".
IW has projects, you can save all the settings as a file, then open it again and simply replace the source PDF.

Acrobat version has presets accessible from the top left menu.
Barcode stores the last settings you used for a symbology, so you don't need to re-configure it again next time, just change the data. Let me know if you need more than that.