We have also run into this roadblock. Luckily we had someone that was capable of coding and created us a "Self Service" portal. Users go there to get apps, books, profiles, etc. Anything that gets installed on the device becomes managed.
I can not think of a workaround for VPP books, but have you tried adding PDF and iBook files into the Meraki MDM app using a "Backpack" configuration profile? Works for some of our needs.
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