I never got it working all over the system in ubuntu 17.10 (I just resigned myself to testing scroll direction in each app), but in 16.04, there were XKB options, Unity settings, separate Gnome settings (because Gnome ignored the X11-level scrolling!), separate KDE settings (though KDE at least obeyed the base X11 options), and at least an app or two that had their own settings, or used some lib that implemented its own scrolling and also didn't have options to control this.
The thing is, though, desktop linux users are just used to this. Your choices boil down to:
1) do a lot of research and setup and then constant maintenance to restore settings that updates casually break, and understand that there will still be exceptions and gaps, or
2) try to stay inside the lines of Gnome, or Unity, or whatever ElementaryOS calls their graphical shell, and ignore the thousands of applications that do not match the look and feel of your chosen environment.
I keep going back and trying desktop linux every few years since switching from Gentoo to Mac in 2003, and sometimes I use it exclusively as my personal machine for months at a time, but in the end, frustration always drives me back into Apple's arms. :(
I don't know what mouse driver I was using (I don't use a touchpad except on laptops, and all my linux machines have been desktops). I would have assumed it was whatever the default was for Ubuntu over the years. :)
(Actually, I do remember that in some versions you had to figure out how to trick the system into thinking you might have a touchpad before it would provide you a place to change the mouse wheel scroll direction, but that seems like a separate failure of preference panels, rather than the root of the issue).
The thing is, though, desktop linux users are just used to this. Your choices boil down to:
1) do a lot of research and setup and then constant maintenance to restore settings that updates casually break, and understand that there will still be exceptions and gaps, or
2) try to stay inside the lines of Gnome, or Unity, or whatever ElementaryOS calls their graphical shell, and ignore the thousands of applications that do not match the look and feel of your chosen environment.
I keep going back and trying desktop linux every few years since switching from Gentoo to Mac in 2003, and sometimes I use it exclusively as my personal machine for months at a time, but in the end, frustration always drives me back into Apple's arms. :(