I think it's a bit of a melodramatic piece, bordering on the paranoia of that shown by Celtic fans.
There are grains of truth in the article but I think it's more the fact that the squeaky wheel gets the grease, and that the OF are more vocal in their objections to the SFA or against other clubs than we or other clubs are.
If anyone at AFC were to make a complaint against Lee McCulloch, as the manager of the club I'd expect it to be Mark McGhee. He didn't, and we move on and accept it as part of football.
I don't think the SFA or SPL favour the OF, just that they are a rather top heavy, incompetent and largely ineffective organisation.