If you want to keep books that you will read with KOReader separate from books that you will use Nickel to read, you could send those books to a hidden directory that is excluded from Nickel's search using the ExcludeSyncFolders in Kobo eReader.conf.
Since I start KOReader and Plato from the Kobo GUI, it's not a real effort for me to safely eject without unplugging the USB cable and then allow import to run before using NickelMenu to trigger a USB connect to allow the metadata update.
Otherwise, you would need to have to create a hidden directory, disable the KoboTouch driver and configure calibre to send to that hidden directory. This would would not allow me to easily compare how books render using Nickel, KOReader or Plato so I've never bothered.
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