The entire game isn't multiplayer only in FSA. You can play by yourself and control all four Links. It is boring, but you still can. Anyways, in the FSA, it basically implies that The Minish Cap is before it, as it refrences the game. And I don't know if I mentioned it here but I think this is the same Link from aLttP. It makes sense too actually. It has the same graphics, the same areas as aLttP, Eastern palace, etc. Also, the story is similar with Zelda and the six maidens being kidnapped again.

Also, I have the game and beaten it many times, and I don't remember seeing Onox, Veran, Twinrova, Phantom Ganon, Agahnim, Shadow Nightmares, or Ganon with the Majora's Mask. I am pretty postive they aren't in the game. I would remember Ganon wearing Majora's Mask. You probably read something wrong.

Anyways, what is funny about FSA, is I was writing the storyline of HoD before the game was released. And I named the aLttP Link, The Hero of Light. Then in FSA, they call the Link, the Hero of Light. I was like, wow, it is like we are in the same wave length. lol. So that is another reason why I think it is the Hero of Light.