configuring /etc/skel manually

Hi all,
I noticed that if I use Pinguy Builder by default, it deletes all my configurations in /etc/skel, syncing, in a limited way, the /home/USER directory with /etc/skel, in this way, the Live ISO created shows a different desktop and a different desktop interface instead my original one.

For this reason, I solved copying manually the following directories from /home/USER to /etc/skel:

.config
.gconf
.kde
.gstreamer-0.10
.gvfs
.local

and all the /home/USER/Desktop icons in /etc/skel/Desktop.

Another issue is the /root cleaning, I disabled it, because it cleans all the settings I did for my Caja file explorer launched in sudo mode, e.g. gksu dbus-launch caja

I'm using Ubuntu 14.04 + Mate 1.81.
Let me know if this is right
Thank you for your precious work!