As discussed elsewhere the key is LOCATION.
Sideloaded kEpubs reside in directories that, depending on your calibre configuration, are based in the root directory of the user partition, and normally based on Author names.
Kobo loaded kEpubs reside in .kobo\kepub.
So you will say, just put sideloaded material in .kobo\kepub.
It's not that simple.
Content located OUTSIDE of the .kobo directory structure is scanned when the device is unplugged and added to the database. This includes entries for the book itself, the cover image, and all entries in the TOC.
Content located INSIDE of the .kobo directory structure is NOT scanned when the device is unplugged and no entries are added to the database. Instead, the database is populated either by Kobo Desktop or the WiFi sync process with the store, depending on what means was used to add the book to the device,
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