You're not missing anything. The data is not easily accessible. Each iOS app maintains a database of its installed books in its own app directory. Individual reader apps each use their own database design to store that information. So the first challenge is finding the database using an app like
iExplorer or
iFunBox, then writing code to extract the booklist from the database.
The second challenge is doing this under program control so that the process can be automated. Due to Apple's 'walled garden' philosophy, it's not possible to simply read the contents of your iDevice without either jailbreaking or using a code library that knows how to get to the individual app directories.
In order to do what you want, a plugin would need to be written using a special code library to peek over the garden wall into the databases for each of those reader apps (and presumably others), returning a list of books with associated metadata to be added as empty books to your calibre library. The required special code library is not currently part of calibre, but may be at some point in the future. Even when that code library becomes available, the plugin would still need to be written by a motivated developer.
To do this on your own today, you would need to do it manually using the tools I mentioned above.
Hope this helps.
G