I'm also having this same issue. BattleEye is unchecked in the config for the cluster, and it has been properly removed on the main server, but it still displays when I bring up my server list to log in. However, I am still able to log in to my cluster server even when I choose to disable BattleEye on my client. At the moment, it just appears to be a cosmetic issue, and doesn't really affect my gameplay as far as I can see.
I used this option for a while on my server, and the only problem I encountered was more of the mismatched mod errors for players, but it wasn't significantly higher. I also didn't notice any real benefit to having it turned on.
Our server was also set up to disable friendly fire, however it just seems the wyvern special attacks just damage everything - players and dinos alike. It appears to be something coded in the creatures themselves.
The only thing that can be done for now is to be very veeery careful.