The extract script does all the unzipping for you and places the games where they need to be.
I’m starting to think you’ve customized your RetroPie and changed something about where things should be, therefore causing these types of problems. Other people have used the script without issue which is why it made it into RetroPie’s main set of scripts.
I cleared out my install of OpenBOR entirely and ran the script and everything compiled and ran and was where it was expected. So I’m wondering if you moved your ROM directory somewhere else instead of symlinking it.