What about using a special file in the main memory directory? I tried it with a modified version of the "copy cover to device" plugin: the main memory has a "system" directory, the memory card has not. Of course: this will only work if there is no system directory on the memory card.
Maybe a special ".is_ebook_reader" file can help, like the ".is_audio_player" used e. g. by banshee (see
https://live.gnome.org/Banshee/Commo...udioPlayerFile). It can be used for organization of directories and prefered file types for this device too.