[Quoth]

MTP is horrible compared to USB Mass Storage. Only one host application can use it over USB at a time.
On Gnome and Cinnamon you can disable automount, so you click on a drive to mount and use filemanager.

But Disabling Automount doesn't disable USB MTP on Mate Desktop, using Caja.
I can unmount my Lenovo Tablet and Alcatel phone etc, and then Calibre loads them. But you can't remount the Mars without unplugging it! Then of course the FileSystem grabs it again.
Some of my gadgets use USB Mass Storage Mode, not MTP.

I found a solution!
0) Do NOT connect the ereader yet!
1) Open System Monitor (can be available via right click just in front of where running windows are listed on a Panel, or via Menu.
2) Select Processes Tab.
3) Scroll down and find "gvfs-mtp-volume-monitor" (clue in name!)
4) Right click and select Stop. Killing is temporary as it will restart.
5) Plug in Mars (or other MTP USB gadget)
6) Run Calibre. It may be slow the FIRST time. Make sure all books on device are in the library and subsequent times it's about as fast as a Kobo H2O original, far faster than Filemanager mode.
7) Either selecting Eject or closing Calibre will end the transfer mode.

Only need to re-enable "gvfs-mtp-volume-monitor" if you need an MTP device in the file manager or for file access. Some Media players that can copy mp3 files can use MTP like Calibre does and will work better in MTP mode than File mode. It will restart at next boot anyway.

Only ONE application can use MTP directly.