@emrecaglar if you need any help to set it up please let me know - I went through some of problems with this combo (it's a bit more problematic than RetroPie for Pi :)).
For sure you can change priviliges for config files as you won't be able to save any config in RetroArch:
sudo chmod -R 777 /opt/retropie/configs/
Please just be mindful that this way you give access to this files and folders to EVERYONE which means that if someone connects to your computer then it has full access to all files and folders in this path.
In my case it does not matter as I don't have constant network access to this device (it sits in arcade cab with no lan/wifi) so not much of a deal for me :)