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If you prefer to sideload via USB, you should be aware that Amazon has gotten into the habit of deleting USB-sideloaded books off your Kindle if you connect to wifi after a period of being offline. The solution is to keep your Kindle permanently offline, without ever connecting to wifi, or not registering it at all (you can't use collections on an unregistered Kindle).
Kobos working better with Calibre means that you can manage metadata (including series info) and collections automatically via Calibre, without any need to do it manually on your device. Kindles don't use series info with sideloaded books at all, so if you want to group your sideloaded books by series, you cannot do that on a Kindle.
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