The same could happen with Dropbox/icloud, or even if you just ran two Minecraft instances with the same copy of the world on one machine - Minecraft worlds are not designed for concurrent modification by multiple processes
They certainly can be. They can be stored wherever you like, either if you are using a modding/hacking launcher (both are very popular for non-technical players, e.g. kids who aren't programmers) or if you are running a minecraft server (the vanilla server jar runs wherever you decide to put it, and doing this is not exactly an esoteric feat; again, nontechnical kids do it.)
So I myself simply sync just one folder with Syncthing, Dropbox style.