Hm, if you don’t want third parties to have access to both servers, I would consider turning one of the Owncloud server instances into a client.
If it’s about redundancy, it might make more sense on a lower level, i.e. file system. But that depends on volume and bandwidth, I think.
From a cloud perspective, I think the warning actually makes sense at that point, since you can very quickly end up with a data loss if another client has access to one of the server files. Even if the probability decreases if you only work alone on the files, this does not necessarily correspond to the cloud approach. I’m sorry that I can’t provide a useful solution without changing the server structure. Maybe someone else.