What I would try first, is making a new extension for those things you want to save in root, then not saving it in backup.
To make an extension, the squashfs-tools-4.0 extension needs to be installed.
Begin by creating directories. Open the Root Terminal and type:
mkdir -p /home/myext/root
Put everything you want saved in root.
To make a extension called "myrootfiles.tcz," open the Root Terminal, and type:
cd /home/myext
mksquashfs root/ myrootfiles.tcz
Put the new extension in the /tce/optional directory. Keep a copy somewhere else, as if you run Update Apps, it may be lost.
Add the name of the new extension to the .dep file of the program that uses these files. (Another option is to add it to On Boot.)
I don't use backup at all. I use persistent /home and /opt, and make extensions for anything else I want saved.