Nop, that's not the solution, the only thing we can do there is just change colors, in case we need to add new <div> or whatever other element we need to modify the core files of the script.
Look at the attached images and you will see what I'm talking about. We were able to add a new theme folder and new style but we needed to modify the DB.
There's no way to control the header, navigation bar, footer, sidebar, etc... without messing the core files.
To avoid this we are doing all the changes using only pure CSS properties directly to our own CSS file under our own theme folder.
We're trying to avoid as much possible that our custom work won't be affected in future updates of the script.