This is really a Bad Idea. You shouldn't need any configuration settings as root besides maybe
your bash profile and what not. Surely you are not running X as root?? Or any GUI mail suites, etc, etc. The only reson to use the root account is to modify the system in ways that is forbidden to users. Otherwise run as user all the time. su to root when necessary. I am sure DE's like KDE and Gnome provide GUI ways to temporarily become root to use certain tuning utilities as well (can't remember, it's been awhile since I used either).
I don't run any X based software as root. Any security flaws they might have will be magnified 100 fold if the user running them is root. I su to root from a command line to modify config files, play with the kernel, etc and then exit back to my user. By trying to combine anything your no_permission_having_user does, with your all_powerful_root_account is again, a Bad Idea
Here is the entire listing of my root ~/
root@tuxbook:~# ls -a
. .bashrc .keep .rnd .xauthC0djVo .xauthYPDPzT .xauthnDsfOX
.. .config .mcop .ssh .xauthKEPXuj .xauthdmmDFy .xauthrmozUS
.ICEauthority .dvdcss .mcoprc .viminfo .xauthM0VzwS .xauthgDjClf .xauthsQiCOW
.Xauthority .fonts.cache-1 .nessusrc .xauth23J5bB .xauthRpAjlA .xauthhHMNXW .xinitrc
.bash_history .hcwd .xauth3jUCgk .xauthUfSJ2t .xauthkzSlB8
Nothing in there my user needs, and no reason for root to have all my X based configs. There are ways to do what your asking, but none are close to being good security practice.