There's a certain integration between FINAL FANTASY XI and PlayOnline that the friend list system uses.
Before they got shut down, I'm pretty sure the custom server project had found a way to isolate the game from playOnline (Naturally, this meant you didn't need to have a paying account to play the game, which hastened its shutdown). I think all they had to do was dummy out all of the stuff that the client checks POL for (e.g. message system, friends). So they could eventually do away with playOnline entirely, but that probably won't happen.

I'm sure that POL will eventually be reduced to nothing more than a game launcher and that some of the nonsense will eventually be cut out of it to make it faster.