Yes, those are mostly dirs. And you can't create them through tmpfiles because it's going to be a mess. But breaking pacman -Qk is relatively harmless, the bigger question is what to do with all the files in var (e.g. exim mailspools)? Wiping /var is not an option on a workstation/server and is OK only in special cases, like kiosk-type systems or Fedora installations (which are broken by default anyway) :).
Let divide the problem, with a package containing /var/lib/prog/ and /etc/prog/conf created by tmpfiles :
- If the program wrote to /var, then there is no problem, as pacman does not remove a non empty dir anyway. - If it doesn't, there is a problem as /var/lib/prog will not be deleted. - The config file will not be deleted by pacman anyway. I can't find a solution now, I will think at it.
systemd's factory reset and atomic upgrades were explicitly stated to be useful only in special situations, like embedded systems. Just because Archlinux systemd package enables them doesn't mean that the entire distribution should be change around.
Being able to just delete /etc/<package> and reboot/restart the program to reset its config isn't "only useful in special situations". As Tobias said, arch is configured by users who can make mistakes. Factory reset isn't only for the entire system. And it doesn't harm the other users.