In Ubuntu 16.10 and earlier natural scroll settings for touchpad were separatefor mouse and touchpad. Since 17.04 there is only one settings so I can't set it differently for diffrent input devices.
using the gsettings command line api, you should be able to access both i.e. these command line commands will get the current values
$ gsettings get org.gnome.desktop.peripherals.mouse natural-scroll
false for me.
$ gsettings get org.gnome.desktop.peripherals.touchpad natural-scroll
Then to change, change the
get argument to
set and pass a value on the end, e.g.
$ gsettings set org.gnome.desktop.peripherals.touchpad natural-scroll true
and obviously repeat the process for the mouse if you want to change that as well.