It is possible to do this with a configuration file on /usr/share/X11/xorg.conf.d/41-libinput-local.conf

these contents work for a specific device:

Section "InputClass"
        Identifier "Logitech USB Receiver Mouse"
        MatchIsPointer "on"
        MatchDevicePath "/dev/input/event*"
        Driver "libinput"
        Option "ScrollButton" "2"
        Option "ScrollMethod" "button"
        Option "NaturalScrolling" "button"
EndSection

It works when the device is hot plugged after the session begins, and it survives during suspend/resume, as reported by Tim.