I use CLFS and use paco (which was written specifically for LFS systems). I start using
paco to log the installation of packages in section 10.5 which is equivalent to the beginning of chapter 6 in LFS. You could then use the -+, --append option to add the configuration files like /etc/group to whichever package you think makes sense or a package that only installs the configuration/miscellaneous files. After you log the installation of the entire system you can use the pacoball utility that comes with paco and create binary packages.
I actually only use paco to log the installation of the base system packages (i.e., I don't create the pacoballs). Once I've installed the base system and verified it works, I create a bzipped tarball of the entire system. I then stick that tarball on one of my other boxes. If I want/need to reinstall the base system I just untar it to a clean partition.