this post is for when you don't have a physical kobo reader
I run both together (Calibre for windows + Kobo windows desktop app) in one Bottle inside Bottles without issues… Works perfectly… I also had to do some configs with it though. If you’re interested I can look into my specific setup later and post it here.
Edit
ah yeah had to insert this variable
Edit Edit
You have to set up your calibre inside bottles like you would with your calibre on windows, so installing the plugins and so on. There is probably a more elegant option with not having to run calibre inside bottles, but this was the quickest thing I landed on