i3 synclient has no natural scrolling
For anyone who comes across this, though synclient has no explicit NaturalScrolling option, it has VertScrollDelta and HorizScrollDelta. Simply setting these to negatives values flips the scroll direction:
synclient VertScrollDelta=-79
synclient HorizScrollDelta=-79
So in your i3 config add:
exec synclient VertScrollDelta=-79 synclient HorizScrollDelta=-79