I think GP misspoke a bit, but the GGP was suggesting to let $HOME point to /home/user, but to put your
actual data in /me. That way apps can "make a mess" in /home/user/.dot-files-galore, while your documents and so on are alone in /me/important-file.txt.
GP then was cautioning that this leaves your most important files at the whims of Unix's simplistic user permissions model, unless you also point systemd and/or AppArmor towards /me.