It varies by desktop. On some you can switch off MTP automount, either in the control panel or filemanager but on some (Mate on Mint) you can't so I use the System Monitor (accessed by right click at start of task buttons on Place bar) pause the gvf-mtp-volume-monitor before connecting USB. Select processes and find it, right click and Stop (not Kill as it would respawn), which is same as Pausing it.
Some MTP devices will be seen by Calibre simply by right-click and eject on the desktop USB gadget device, works for ancient Sony phone but not Boyue Mars as it can't remount without cable removal and re-insertion after an eject on desktop.
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