I have found a workaround that seems to solve the issue in Xenial 16.04.
Credit goes to: 
https://forums.linuxmint.com/viewtopic.php?f=90&t=233135&p=1236836&sid=394bf7ad96c3ba102949bac4dd404a1a

In short, run in a terminal:
$ synclient

It will output a list of key-value pairs, search the key: 'VertScrollDelta' and 
check its value.
If its e.g. 56, set then it to -56 with the following command:

$ synclient VertScrollDelta=-56

If you want to do the same with the horizontal scroll, search instead
for the key: 'HorizScrollDelta' and invert it in the same way as you did
before

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

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

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