I imagine the situation with Fear/Mason was handled way earlier then the public announcement. As an organization EG were probably working on two paths, get Fear rehabilitated so he can play while also telling valve that Mason would take his place (way before they announced it to the public), that way they're covered no matter what. So Fear is ready to play but they've already told Valve they've got a stand in.... and if Valve said it's too late the change the roster then it would explain a lot about this current situation.
Mason gets officially added to EG, Fear is not happy and trying to get into TI anyway he can (Playing for NAR, Casting, Coaching, whatever), and Era is not allowed to have a stand in, because they've already said it's too late to change your roster. The mistake they made was not communicating any of what was actually happening to the audience, which is fucking super surprising coming from Valve am I right?
I think what they should do, at this point, is allow fnatic (or anybody really) to play in TI with no more then one stand in. They've already let EG do this, and even if behind the scenes the circumstances are different, in front of the scenes it will look unfair.
They need to clarify and publish comprehensive tournament regulations ahead of time for TI5 to keep something like this from happening again, but for TI4 it's too late.
All of their problems/drama/controversy or whatever you want to call it, could be handled with better public relations. Maybe they should spend some of those millions of dollars to better communicate with the people who gave it to them.