I use Mate on Mint. I have to pause the "gvfs-mtp-volume-monitor" via right click "Stop process" in System Monitor -> Processes for some Android devices. Some MTP devices work if I right click on desktop icon for the device and "Unmount", but others don't.
You can change control panel settings if using Cinnamon to disable filesystem automount, but that does nothing on Mate (combination of caja file explorer and how gvfs-mtp works.
You can "Continue" the process after eject from Calibre and disconnection. Don't "kill" or "End Process" of "gvfs-mtp-volume-monitor" or it will automatically respawn.
Windows used to have the same problem but now there is an extra layer of driver to "share" the MTP filesystem on windows. It's a horrible system, possibly designed for the Zune.
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