Xconfigurator always adds a ZAxisMapping to /etc/X11/Xf86Config-4, whereas
for /etc/X11/XF86Config it only adds one for wheelmouse, which seems to
make more sense.
The new behaviour is by design ("It shouldn't make anything not work would it.
but it would make sense for all wheel mouse? It shouldn't do any damage, and it
would solve the problems of the wheel not working... OK - do it then")
Well it could cause problems with real 4 button mouse (the logitech onces with a
thump button, although that should be really mapped to 7 then I guess)
Besides that it is not consistent between XF3.3 and XF40, for XF3.3 it is only
added when there is a wheelmouse, for XF40 it is always selected.
But it is your call.