ADE's limitations are spelled out in its HELP section. It is intended for
individual users and pleasure reading, not adademicians or heavy users of
research materials. So in that sense, you are correct in 'exposing' its
limitations. Simply put, I think you've chosen the wrong tool, but the
tool you chose works wonderfully within its parameters. And although I
have no connection with Adobe, I doubt very much that they would consider
expanding ADE's capabilities to cover your scenario. They have enough
challenges keeping up with the technology within their envelope.
Most libraries use Overdrive software, and that may do the trick for you.
There are other offerings available that you could try, such as Calibre or
Bluefire Reader, that may have fewer limitations in your environment. Many
academic communities I know of use other software as well. I'd contact
the library/sources that you're dealing with and see if there's an
alternative that will work better for you.