Believe me or not but the local representatives for this printer manufacturer recently advised that, when it turns to send a JDF and a related PDF to this very Front End, then the only solution was to merge both files into a single file, then submit.
So, we had to develop some automation for our customer.
Obviously, it's then impossible to view the resulting file in Acrobat Reader or another PDF Viewer application - as they think that the file has been corrupted, due to the unexpected XML/JDF header.
But based on our experience, the Front End and the printer then follow the JDF directions and print the PDF accordingly.
Unfortunately, the above only concerns regular (Adobe) PDF documents - we did not experiment PDF/VT, as in your case.