Regarding your solution: this cannot actually work as expected. If you rename the folder then the link will just point to a non-existing folder, causing Factorio to just not load any mods. Of course this would get rid of the error message, but if you are certain the mod was still loaded I am really confused.
Edit: nevermind, I forgot we are talking about Factorio for a second. Of course the devs have posted a full documentation of the format used: viewtopic.php?t=59851
It will take longer to implement this way but it will be a lot more robust.