Okay, after toying with this for a while I have found a rather convoluted work around that is not a mass deployment solution by any means.
Systems Manger --> VPP--> Add User
Instead of adding the Apple ID, add by the email address.
Instruct end user that when they get the link, they must log in via their Apple Managed ID (not a personal account).
After they do this, you can assign and push them books. They will not auto-deploy, they must open iBooks and then download.
This is not a universal solution for me as I have elementary students who do not all have email addresses. We also have shared carts.
I cannot imagine the problem for those who have already associated a work email as an Apple ID.