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. :(
In any gnome 3 distro I've ever used, I've only ever had to change it in the gnome control center and it works system wide.
Right now I'm running solus mate and changing it in the mate mouse and touchpad settings is system wide and works in both qt and gtk apps...
Were you using a touchpad driver other than libinput?
(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).