My personal solution in 'Xubuntu 17.10' (works fine in all GTK2/3
software)

>> 1 >> Looking for the Device-ID with...

:~$ xinput list

 ⎡ Virtual core pointer                         id=2    [master pointer  (3)]
 ⎜   ↳ Virtual core XTEST pointer               id=4    [slave  pointer  (2)]
 ⎜   ↳ Logitech MX Anywhere 2                   id=8    [slave  pointer  (2)]
 ⎜   ↳ Logitech Unifying Device. Wireless PID:404d      id=9    [slave  pointer 
 (2)]
 ⎣ Virtual core keyboard                        id=3    [master keyboard (2)]
     ↳ Virtual core XTEST keyboard              id=5    [slave  keyboard (3)]
     ↳ Power Button                             id=6    [slave  keyboard (3)]
     ↳ Power Button                             id=7    [slave  keyboard (3)]
     ↳ Logitech MX Anywhere 2                   id=10   [slave  keyboard (3)]
     ↳ Logitech Unifying Device. Wireless PID:404d      id=11   [slave  
keyboard (3)]


>> 2 >> enable natural scrolling with...(change the ## to your Device-ID)
 
:~$ xinput --set-int-prop ## "libinput Natural Scrolling Enabled" 8 1 


So in my case: xinput --set-int-prop 8 "libinput Natural Scrolling Enabled" 8 1

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https://bugs.launchpad.net/bugs/1368402

Title:
  GTK3 apps doesn't understand natural scrolling in Xubuntu

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