You could experiment with a feature added in Calibre 8.x that allows you to use the Connect to Folder option and specify connect as a device.
What you would have to do is with your Kobo attached to your laptop create a Windows share pointing to the Kobo directory. Then on your containerised Calibre access that Windows share as the target in Connect to Folder specifying that calibre should consider this as a Kobo Clara.
I can't guarantee this will work (or even provide steps on how to access a Windows share from the containerised Calibre).
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