
Kobo has its own Library manager (not filename based).
To begin: Don't try an fight/trick it.

(once you get comfortable, then go for optional methods)
Remember,
a stock Kobo takes 2 Calibre
connect sessions to complete the metadata absorption.
Connect #1: File (book) transfer
Eject (Disconnect) #1: Book absorption (processing) : This makes the initial internal Database entries.
Connection #2: Populate the Database with additional metadata (This is automatic. You just connect and wait for calibre Jobs to be done).
Eject (disconnect) #2
IMHO Get the Kobo Utilities and Kobo Utilities Extended edition plugins for Calibre. Look at all the configuration settings to see what each can do.
Note: There is a setting that allows for custom
per device (if you have more than 1 Kobo)
Note2: There are 2 places to customize if using the Extended mode: The second is on the Driver MENU of Kobo Utilities.