I've happened upon a strange bug. While using this patch on a FTB ultimate server hosted on my Linux machine, the server will create ee3's config file in the root folder of the server and not the config/ee3/ folder. Instead, the server creates the file config/ee3/ee3.cfg or something else that's completely wrong, and my client will warn me of a worldID mismatch on the server when I try to log on and it'll kick me off.
But I found a fix. I had to copy and paste the config file that my client created when installed with this patch (that's in config/ee3/) into the correct directory on my server (again, config/ee3/). I haven't tested the original ee3.jar file on my Linux machine before patching, but this ordeal leads me to believe that this patch alters where it will create the config in Linux and how it does but won't alter where the mod looks for the config. As far as I can tell, this patch doesn't mess with the way my server can do things on Windows, just Linux; as it caused no errors on my own Windows 7 machine.