When I open a file with root gedit I'd like to have the same setup as my normal gedit. So theme, preferences, and addons.
Can I set up some sym links in the right spot to achieve this?
I think this is quite impossible because gedit manages its settings through gconf and to sync these it would require a gnome-settings-deamon running for root.
You normally wouldn't synchronize normal gedit settings with root gedit user settings.
Root has its own settings, and the computer user has his own settings. The two are not the same. This is by design.
When you are operating as root, you are using the root user's profile, and when you're operating as yourself, you're using your personal profile. Each has its own permissions and ownership, tied to that particular account. They're not intended to be the same.