https://bugzilla.gnome.org/show_bug.cgi?id=750994
There are no plans for a fix. The maintainer recommends waiting for Wayland.
It seems to boil down to an issue in the underlying X11 machinery and it would need to be fixed there first to build a basis on which proper fixes can be implemented.
Given that X11 is in maintenance mode (and as its fans keep saying: It works perfectly fine and doesn't need any more work done on it), it's not likely that's happening.
So, yes, given that information (and I just arrived at that bug report through your post), I would indeed say that waiting for Wayland is the only option they have. All other attempts ended up causing worse issues.
The issue comes from XInput2 (https://www.x.org/releases/X11R7.7/doc/inputproto/XI2proto.t...)
So I guess the "fix" would be to have two completely separate input handlers on X11, one of which supporting smooth scrolling and multitouch, the other not and then offering users a toggle in the style of
[ ] do not ignore the first scroll input after focus loss, but disable smooth scrolling and multitouch
Plus handling all the potential issues by having two separate input handlers.
That's asking a bit much for this particular issue und greatly smells like a case of XKCD 1172