You shouldn't experince any problems with what the program did to your registry.
If for some odd and peculiar reason you experince problems due to the changes the program made in the registry, (which you shouldn't), you can simply backup your registry from the backup you made earlier.
What the program did was modify your "Current Version" Key/Folder to the proper manner. It directs the computer to look for the Registered Owner in the directory CurrentVersion/RegisteredOwner. The program has not made any changes that should affect any other part of the computer.
It says you cant change it because so many other folders use it as a root directory. I do not think you can change it, however I will play around with other things to see if their is a way to change it.