The script doesn't come from systemd but from the iptables package, which is from Arch. Maybe at the time the service was written that was the original location till arch made the systemd subdirectory. So either iptables needs repackaging by Obarun or the script adjusted to the current location. I would much rather not have any directory in the system labeled systemd.
The packman script prevents any such intruder to go into the system and totally break it. For onething it will replace the /sbin/init link and it will boot with systemd, but it will conflict with 2 tons of other stuff that systemd had no business to replace. It will also create a plethora of useless system users that will not be removed after you remove systemd and reinstall s6 (the 2 conflict, at /usr/bin/{init,poweroff,reboot,halt,shutdown} at least. So you really can't force install systemd till s6 is completely removed.
If you run:
pacman -Ql iptables | grep flush
/usr/lib/systemd/scripts/iptables-flush
so the script is there without systemd being present, but you are right the service is written wrong.
Till someone fixes it (boot@ -66serv) you can copy the service from /usr/lib/66/service/..... /etc/66/service and edit the environment link to the correct one. Otherwise give a little time for the devs to make adjustments. I would go to the git and write a correction and make a commit for the change, but the cleaner solution is to repackage iptables, and 45 other arch packages.
If arch made this move recently in this package they probably have done it across the board for many others. One can only find this out by making a some extensive arch installation and see what falls in that "hole". From my system it seems as the creation of those directories came Dec20, Jan and Feb. And there is tons of this crap in them.
On the other hand this is an environment definition, the package itself being an arch package, knows the correct definition of the location of the script. So I doubt it is producing an error.
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