The files under /etc/ usually should be set by CONFFILES, this is good for package manager.
As discussed previously, starting here: http://lists.openembedded.org/pipermail/openembedded-core/2014-December/thread.html#100001 and answered here: http://lists.openembedded.org/pipermail/openembedded-core/2014-December/100006.html we can't declare all of /etc/ to be CONFFILES. As Mike Looijmans said: FHS may have written that somewhere, but if you just take a quick look at what is in /etc/, you'll find that actual configuration files are quite rare, but there are tons of scripts and distro related files there. Whether or not a file there is supposed to be edited by the end-user is something of a distro decision. Also, "configuration file" does not necessarily mean that the USER is in control. A configuration file may also simply distinguish machine capabilities or software features. We'll end up having to patch hundreds of recipes with a CONFFILES="" or similar line. So I'm closing the enhancement. If you have a more narrowly specified idea, please open a new enhancement.
See previous comment.