Some etc-updates simply should not exist. Case in point: /etc/fstab is, more often than not, a file that is set once, and never again touched. The last etc-update to fstab changed a comment in it, which is highly unnecessary for the performance of a linux system. /etc/fstab does not need to be updated unless some fundamental change in gentoo has happened - and, to do so(since most average users just auto-merge because an interactive merge takes too long) is dangerous, even - especially if the user uses their system as a server - the next time the system has to be rebooted, from anywhere, it won't boot. /etc/samba/smb.conf does not need to be updated. Especially to an empty file. It takes a long time to work on a smb.conf sometimes(esp when tweaking settings). Fortunately, some of us are careful and keep backups, but not everybody does. It is a bug to have any config file "updated" to a blank file, not an optimization. /etc/security/selinux/src/policy/Makefile - maybe there should be a flag on the cfg_blahblah file name as to the severity of the update on the overall system. SELinux policies are another thing that updates should be careful of. Most users don't spend too much time on them(since gentoo takes care of a lot of details), but some users, like myself, like to customize SELinux policies, It kindof sucks to have to revert everything to a backup because etc-update indiscriminately updates everything without question(unless you use -3, which not everyone has time for - esp when the server is just one of many). Please use discretion when choosing updates. If you're going to "update" a file to a blank, please don't. If you're going to update a file that is usually just set once and forgotten about, maybe put a flag on the filename to notify the user, regardless of what he chooses(-3 or -5).
Don't touch the restrict checkboxes... /etc/fstab is NEVER updated. As for the rest, you can defer them as you wish by not running etc-update or dispatch-conf and break up the pieces when something breaks (pretty much granted with udev/baselayout updates). Also, have a look at dispatch.conf and /etc/dispatch.conf.conf for backups, updates automation etc. etc. etc.
Err, dispatch-conf and /etc/dispatch-conf.conf that is...
/etc/fstab WAS updated in the last 'emerge -u world' I did, and etc-update would have replaced it, had I not seen it in my list of updates(it's been a while since I've done /etc/update, so I had quite a bunch of updates to do...I didn't think fstab would be in there, and I don't know why it was).