But isn't the PaperWhite USB Mass Storage?
It should be visible in filemanager. If not try another port or cable.
For USB-MTP (All Android since about version 4?)
I stop, not End or Kill, the gvfs-mtp-volume-monitor before USB connection and continue it (both with Right Click Menu) after eject, because Caja on Mate desktop can't be prevented from automount. Some MTP USB devices can be unmounted and then Calibre can connect but others don't work.
Some desktops and/or filamanagers have a setting to never automount.
I've never had any problem with PW3, Basic, Oasis, KK3, DXG on Linux, or Nook ST, Sony PRS350, Sony T1, Kobo Touch, H2O, Libra, Sage, Elipsa, Nia, Libra 2 or Y-Ben P47L as those are all mass storage mode, not MTP.