Comment 74 for bug 792085

I found two workarounds.

Workaround 1)
On Xubuntu 14.10 using Thunar 1.6.3 file manager I managed to stop the automatic remount of unmounted USB 3.0 drives using USB 3.0 ports.
In Thunar: Edit -> Preferences -> Advanced -> "Configure the management of removable drives and media." -> "Storage" tab:
I unchecked the "Mount removable drives when hot-plugged" option.
With this setting, after unmounting the USB 3.0 device in Thunar, 'dmesg | grep USB' has these new lines:
[ 1902.911399] usb 4-3: USB disconnect, device number 7
[ 1903.395819] usb 4-3: new SuperSpeed USB device number 8 using xhci_hcd
[ 1903.412365] usb 4-3: New USB device found, idVendor=174c, idProduct=55aa
[ 1903.412379] usb 4-3: New USB device strings: Mfr=2, Product=3, SerialNumber=1
[ 1903.413049] usb-storage 4-3:1.0: USB Mass Storage device detected
The USB 3.0 external HDD stops for a second and starts spinning after that (like before unchecking the mentioned preference), the device can be seen in /dev/ but is not mounted. As a side-effect of this, thunar doesn't automount drives plugged in.

Workaround 2)
Instead of using the eject buttons, right-click -> "Unmount" each partition of the device in the file manager (I tested this with Thunar).

Screenshots available at https://www.dropbox.com/sh/iax2x6by866nbtq/AADd3ljfdAn2ljqkZrJg0Spda?dl=0