The only other driver that manages an on device database is the sony driver. At least for the older devices (before the T1) the driver scans both the actual files and reads the device db and metadata.calibre. It then populates the metadata from those three sources. IIRC the device db has the lowest priority. So files on the device are always shown as on device regardless of their status in the device db. This has never been a problem with the SONYs as they are a lot more robust than the Kobos.
There are two possibilities that come to mind:
1) Use your custom collection
2) Add some way for the device driver system to signal to the GUI that the book is not recognized by the device, the gui could then use an exclamation mark instead of a tick to indicate such problem books.
(1) you can do yourself, (2) will require some work either from chaley or me. I cant speak for Charles, but I am rather busy at the moment, so if you want to pursue (2) you might have to wait a few days.
Personally, I prefer (2)