FWIW, besides extra metadata that was where local user and device specific DRM info was stored. That way there was room for multiple user keys. In actuality only a single key per book was used for text encryption but that key was encrypted so that only a device or user key could get decrypt it to access it And all of that took space. But that was a long time ago, so things have probably changed considerably.
It was actually quite smart as the book's text could be encrypted once independently of user or device but that key was itself encrypted by user specific keys that could be written on the fly as the book was downloaded very very quickly.
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