There is no such term “optified Linux system”. There is a term “Nokia's engineers”. I didn't say what to do, I told the basics of filesystem hierarchy. And the one of the basics is that package management system should not touch users home directories. Of course on maemo there is /opt, in which you have to put large files to not to wipe free space on rootfs (and make symlinks in proper places). But this package contain only few little scripts which won't affect free space on rootfs at all. As for $HOME/.blahblah, these directories are for user-specific configuration files. Again, /etc is for system-wide configuration files.