I could change the script, so all background files come in that directory.
It could be good, because like that, you will use the default Retroarch overlay folder for Retropie.
Ok, I will make a commit when I can.
Then I will remove the subdirectory's also.
All overlays are saved in /opt/retropie/configs/all/retroarch/overlay
Basically it will look like the artwork directory but then containing .cfg and .png.
I was able to do a commit on github.
I did the change without testing, but should work. (did test : OK)
If you comment part 2 and 3 in the script it will not download all again.
I think you know how to do that.
You have to manually remove /home/pi/RetroPie/overlays.